Starting phenix.real_space_refine on Thu Aug 6 09:49:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umf_42378/08_2026/8umf_42378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umf_42378/08_2026/8umf_42378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8umf_42378/08_2026/8umf_42378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umf_42378/08_2026/8umf_42378.map" model { file = "/net/cci-nas-00/data/ceres_data/8umf_42378/08_2026/8umf_42378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umf_42378/08_2026/8umf_42378.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 172 5.49 5 Mg 7 5.21 5 S 37 5.16 5 C 8725 2.51 5 N 2621 2.21 5 O 3242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14804 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1376, 11159 Classifications: {'peptide': 1376} Link IDs: {'PTRANS': 38, 'TRANS': 1337} Chain breaks: 3 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2568 Classifications: {'RNA': 121} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 58, 'rna3p_pyr': 48} Link IDs: {'rna2p': 15, 'rna3p': 105} Chain: "C" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 395 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "E" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.57, per 1000 atoms: 0.17 Number of scatterers: 14804 At special positions: 0 Unit cell: (91.53, 113.4, 139.32, 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 37 16.00 P 172 15.00 Mg 7 11.99 O 3242 8.00 N 2621 7.00 C 8725 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: 0.86 Conformation dependent library (CDL) restraints added in 430.4 milliseconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 10 sheets defined 55.3% alpha, 10.3% beta 65 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 50 through 82 Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.518A pdb=" N LEU A 114 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 removed outlier: 3.775A pdb=" N PHE A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 123 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 148 Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'A' and resid 181 through 200 removed outlier: 3.632A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.651A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 248 Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 260 through 266 removed outlier: 3.634A pdb=" N ASN A 265 " --> pdb=" O SER A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 290 through 303 removed outlier: 3.541A pdb=" N ASN A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 350 through 361 removed outlier: 3.841A pdb=" N ILE A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 397 through 412 Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 432 through 448 removed outlier: 4.025A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 471 Processing helix chain 'A' and resid 472 through 477 removed outlier: 5.426A pdb=" N PHE A 475 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 506 removed outlier: 3.556A pdb=" N ARG A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 526 through 541 Processing helix chain 'A' and resid 543 through 557 Processing helix chain 'A' and resid 562 through 586 Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 620 through 632 Processing helix chain 'A' and resid 652 through 674 Processing helix chain 'A' and resid 699 through 707 removed outlier: 4.281A pdb=" N LYS A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 738 removed outlier: 3.834A pdb=" N SER A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 769 Processing helix chain 'A' and resid 774 through 776 No H-bonds generated for 'chain 'A' and resid 774 through 776' Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 800 through 809 Processing helix chain 'A' and resid 812 through 826 Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'A' and resid 835 through 838 Processing helix chain 'A' and resid 839 through 849 Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 856 through 866 removed outlier: 3.561A pdb=" N ARG A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 873 Processing helix chain 'A' and resid 877 through 893 Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 920 through 928 Processing helix chain 'A' and resid 929 through 932 Processing helix chain 'A' and resid 940 through 956 removed outlier: 4.102A pdb=" N HIS A 944 " --> pdb=" O PRO A 940 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 removed outlier: 4.092A pdb=" N VAL A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 981 removed outlier: 3.588A pdb=" N ASN A 976 " --> pdb=" O ALA A 972 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1007 Processing helix chain 'A' and resid 1046 through 1052 Processing helix chain 'A' and resid 1074 through 1088 removed outlier: 3.683A pdb=" N PHE A1086 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1104 Processing helix chain 'A' and resid 1126 through 1131 Processing helix chain 'A' and resid 1132 through 1135 Processing helix chain 'A' and resid 1156 through 1166 removed outlier: 4.075A pdb=" N GLU A1160 " --> pdb=" O PRO A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1197 removed outlier: 3.529A pdb=" N LEU A1192 " --> pdb=" O ASP A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1333 Processing helix chain 'A' and resid 1338 through 1342 Processing helix chain 'A' and resid 1349 through 1361 Processing helix chain 'A' and resid 1368 through 1370 No H-bonds generated for 'chain 'A' and resid 1368 through 1370' Processing helix chain 'A' and resid 1392 through 1409 removed outlier: 3.597A pdb=" N GLN A1409 " --> pdb=" O VAL A1405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 903 through 912 removed outlier: 3.906A pdb=" N GLU A 690 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 35 " --> pdb=" O ASN A 989 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE A 991 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL A 37 " --> pdb=" O ILE A 991 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521 removed outlier: 7.110A pdb=" N SER A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 754 through 757 Processing sheet with id=AA5, first strand: chain 'A' and resid 1215 through 1218 removed outlier: 6.411A pdb=" N ASN A1110 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ILE A1014 " --> pdb=" O ASN A1110 " (cutoff:3.500A) removed outlier: 13.686A pdb=" N SER A1112 " --> pdb=" O GLU A1012 " (cutoff:3.500A) removed outlier: 18.968A pdb=" N GLU A1012 " --> pdb=" O SER A1112 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLY A1013 " --> pdb=" O MET A1243 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET A1243 " --> pdb=" O GLY A1013 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A1241 " --> pdb=" O PHE A1015 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU A1017 " --> pdb=" O TYR A1239 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N TYR A1239 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 15.770A pdb=" N PHE A1019 " --> pdb=" O ASP A1237 " (cutoff:3.500A) removed outlier: 20.399A pdb=" N ASP A1237 " --> pdb=" O PHE A1019 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1040 through 1042 Processing sheet with id=AA7, first strand: chain 'A' and resid 1117 through 1118 Processing sheet with id=AA8, first strand: chain 'A' and resid 1137 through 1141 Processing sheet with id=AA9, first strand: chain 'A' and resid 1266 through 1267 removed outlier: 7.788A pdb=" N LEU A1266 " --> pdb=" O LYS A1250 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN A1288 " --> pdb=" O VAL A1254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1296 through 1297 removed outlier: 6.555A pdb=" N LYS A1383 " --> pdb=" O ILE A1376 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N CYS A1387 " --> pdb=" O GLN A1372 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN A1372 " --> pdb=" O CYS A1387 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 160 hydrogen bonds 302 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 119 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2957 1.33 - 1.45: 4318 1.45 - 1.57: 7754 1.57 - 1.69: 341 1.69 - 1.81: 57 Bond restraints: 15427 Sorted by residual: bond pdb=" C1' DT C 44 " pdb=" N1 DT C 44 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.67e+01 bond pdb=" C3' DC C 59 " pdb=" C2' DC C 59 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.77e+00 bond pdb=" C3' DG E 24 " pdb=" C2' DG E 24 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.58e+00 bond pdb=" N9 A B 80 " pdb=" C4 A B 80 " ideal model delta sigma weight residual 1.374 1.391 -0.017 6.00e-03 2.78e+04 8.45e+00 bond pdb=" C4' DC D 38 " pdb=" C3' DC D 38 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.00e-02 1.00e+04 8.17e+00 ... (remaining 15422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 20495 1.92 - 3.83: 1001 3.83 - 5.75: 93 5.75 - 7.66: 21 7.66 - 9.58: 9 Bond angle restraints: 21619 Sorted by residual: angle pdb=" C3' C B 57 " pdb=" O3' C B 57 " pdb=" P U B 58 " ideal model delta sigma weight residual 119.70 127.50 -7.80 1.20e+00 6.94e-01 4.23e+01 angle pdb=" O4' G B 15 " pdb=" C1' G B 15 " pdb=" N9 G B 15 " ideal model delta sigma weight residual 108.20 113.36 -5.16 8.00e-01 1.56e+00 4.16e+01 angle pdb=" N1 C B 103 " pdb=" C2 C B 103 " pdb=" O2 C B 103 " ideal model delta sigma weight residual 118.90 122.63 -3.73 6.00e-01 2.78e+00 3.86e+01 angle pdb=" N1 C B 96 " pdb=" C6 C B 96 " pdb=" C5 C B 96 " ideal model delta sigma weight residual 121.00 123.97 -2.97 5.00e-01 4.00e+00 3.54e+01 angle pdb=" N1 U B 4 " pdb=" C6 U B 4 " pdb=" C5 U B 4 " ideal model delta sigma weight residual 122.70 125.58 -2.88 5.00e-01 4.00e+00 3.33e+01 ... (remaining 21614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 8827 35.51 - 71.02: 477 71.02 - 106.53: 45 106.53 - 142.03: 1 142.03 - 177.54: 5 Dihedral angle restraints: 9355 sinusoidal: 5304 harmonic: 4051 Sorted by residual: dihedral pdb=" O4' U B 101 " pdb=" C1' U B 101 " pdb=" N1 U B 101 " pdb=" C2 U B 101 " ideal model delta sinusoidal sigma weight residual 200.00 50.64 149.36 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' U B 108 " pdb=" C1' U B 108 " pdb=" N1 U B 108 " pdb=" C2 U B 108 " ideal model delta sinusoidal sigma weight residual -128.00 49.54 -177.54 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 85 " pdb=" C1' U B 85 " pdb=" N1 U B 85 " pdb=" C2 U B 85 " ideal model delta sinusoidal sigma weight residual -128.00 47.17 -175.17 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 9352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1893 0.057 - 0.115: 435 0.115 - 0.172: 167 0.172 - 0.230: 13 0.230 - 0.287: 2 Chirality restraints: 2510 Sorted by residual: chirality pdb=" CB THR A1381 " pdb=" CA THR A1381 " pdb=" OG1 THR A1381 " pdb=" CG2 THR A1381 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C3' C B 57 " pdb=" C4' C B 57 " pdb=" O3' C B 57 " pdb=" C2' C B 57 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL A 575 " pdb=" CA VAL A 575 " pdb=" CG1 VAL A 575 " pdb=" CG2 VAL A 575 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2507 not shown) Planarity restraints: 2136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 15 " 0.058 2.00e-02 2.50e+03 2.46e-02 1.82e+01 pdb=" N9 G B 15 " -0.058 2.00e-02 2.50e+03 pdb=" C8 G B 15 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G B 15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 15 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 15 " 0.009 2.00e-02 2.50e+03 pdb=" O6 G B 15 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G B 15 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G B 15 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G B 15 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 15 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G B 15 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 99 " -0.046 2.00e-02 2.50e+03 1.93e-02 1.12e+01 pdb=" N9 G B 99 " 0.045 2.00e-02 2.50e+03 pdb=" C8 G B 99 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G B 99 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 99 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G B 99 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 99 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G B 99 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G B 99 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G B 99 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 99 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G B 99 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 106 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C GLU A 106 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU A 106 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 107 " -0.017 2.00e-02 2.50e+03 ... (remaining 2133 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 315 2.65 - 3.21: 12606 3.21 - 3.77: 26154 3.77 - 4.34: 36347 4.34 - 4.90: 54274 Nonbonded interactions: 129696 Sorted by model distance: nonbonded pdb=" OD1 ASP A 756 " pdb="MG MG A1503 " model vdw 2.087 2.170 nonbonded pdb=" OD2 ASP A 10 " pdb="MG MG A1502 " model vdw 2.102 2.170 nonbonded pdb=" OP1 DC C 43 " pdb="MG MG A1502 " model vdw 2.125 2.170 nonbonded pdb=" OP2 DC C 43 " pdb="MG MG A1501 " model vdw 2.142 2.170 nonbonded pdb=" OG SER A 94 " pdb=" OP1 A B 72 " model vdw 2.189 3.040 ... (remaining 129691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 6.490 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.230 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.005 0.057 15427 Z= 0.357 Angle : 0.877 9.576 21619 Z= 0.650 Chirality : 0.056 0.287 2510 Planarity : 0.005 0.044 2136 Dihedral : 19.052 177.543 6727 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.20 (0.21), residues: 1368 helix: -0.80 (0.17), residues: 673 sheet: -0.23 (0.42), residues: 155 loop : -0.72 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 527 TYR 0.027 0.002 TYR A 819 PHE 0.022 0.002 PHE A 242 TRP 0.018 0.002 TRP A 516 HIS 0.009 0.002 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.36 (15427) covalent geometry : angle 0.87735 / 0.65 (21619) hydrogen bonds : bond 0.13890 / 9.11 ( 721) hydrogen bonds : angle 6.62360 / 4.77 ( 1898) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.510 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 106 average time/residue: 0.7148 time to fit residues: 82.1487 Evaluate side-chains 57 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 1047 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.108288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.080671 restraints weight = 27918.843| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.29 r_work: 0.3015 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15427 Z= 0.160 Angle : 0.591 7.751 21619 Z= 0.335 Chirality : 0.041 0.328 2510 Planarity : 0.004 0.040 2136 Dihedral : 20.670 178.800 3904 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.14 % Allowed : 6.17 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.16 (0.22), residues: 1368 helix: 0.33 (0.19), residues: 679 sheet: -0.09 (0.41), residues: 150 loop : -0.51 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 518 TYR 0.018 0.001 TYR A 767 PHE 0.019 0.001 PHE A 160 TRP 0.008 0.001 TRP A 355 HIS 0.004 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (15427) covalent geometry : angle 0.59060 / 0.33 (21619) hydrogen bonds : bond 0.05027 / 3.32 ( 721) hydrogen bonds : angle 4.91507 / 3.57 ( 1898) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.502 Fit side-chains REVERT: A 158 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: A 413 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8475 (ttp-170) REVERT: A 440 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: A 702 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7691 (tm-30) REVERT: A 982 GLN cc_start: 0.7734 (pp30) cc_final: 0.7519 (pp30) outliers start: 14 outliers final: 5 residues processed: 69 average time/residue: 0.5559 time to fit residues: 42.8440 Evaluate side-chains 60 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 767 TYR Chi-restraints excluded: chain A residue 926 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 95 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.105039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077107 restraints weight = 28352.279| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.28 r_work: 0.2943 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15427 Z= 0.261 Angle : 0.618 6.951 21619 Z= 0.342 Chirality : 0.044 0.352 2510 Planarity : 0.004 0.043 2136 Dihedral : 20.521 177.905 3900 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.46 % Allowed : 8.37 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.18 (0.22), residues: 1368 helix: 0.71 (0.20), residues: 681 sheet: -0.19 (0.42), residues: 155 loop : -0.40 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 255 TYR 0.017 0.002 TYR A 281 PHE 0.023 0.002 PHE A 242 TRP 0.010 0.001 TRP A1035 HIS 0.008 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.26 (15427) covalent geometry : angle 0.61797 / 0.34 (21619) hydrogen bonds : bond 0.05049 / 3.35 ( 721) hydrogen bonds : angle 4.74229 / 3.44 ( 1898) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.457 Fit side-chains REVERT: A 413 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8469 (ttp-170) REVERT: A 440 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: A 702 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 982 GLN cc_start: 0.7767 (pp30) cc_final: 0.7507 (pp30) outliers start: 18 outliers final: 8 residues processed: 70 average time/residue: 0.5775 time to fit residues: 45.0261 Evaluate side-chains 63 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 767 TYR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1009 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 28 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 133 optimal weight: 0.0010 chunk 9 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 HIS ** A1392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.107863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.080197 restraints weight = 28155.476| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.30 r_work: 0.3008 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15427 Z= 0.134 Angle : 0.530 9.583 21619 Z= 0.302 Chirality : 0.039 0.354 2510 Planarity : 0.003 0.030 2136 Dihedral : 20.541 178.027 3900 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.38 % Allowed : 9.59 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.54 (0.23), residues: 1368 helix: 1.05 (0.20), residues: 682 sheet: -0.20 (0.41), residues: 155 loop : -0.24 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1198 TYR 0.049 0.002 TYR A 767 PHE 0.015 0.001 PHE A 242 TRP 0.006 0.001 TRP A 338 HIS 0.003 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (15427) covalent geometry : angle 0.52971 / 0.30 (21619) hydrogen bonds : bond 0.04480 / 2.96 ( 721) hydrogen bonds : angle 4.45944 / 3.24 ( 1898) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8357 (pm20) REVERT: A 413 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8405 (ttp-170) REVERT: A 440 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: A 702 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 982 GLN cc_start: 0.7803 (pp30) cc_final: 0.7502 (pp30) outliers start: 17 outliers final: 7 residues processed: 76 average time/residue: 0.5240 time to fit residues: 44.7378 Evaluate side-chains 60 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1381 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 138 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.107097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.079533 restraints weight = 28205.507| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.28 r_work: 0.2994 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15427 Z= 0.159 Angle : 0.531 8.627 21619 Z= 0.299 Chirality : 0.039 0.353 2510 Planarity : 0.003 0.029 2136 Dihedral : 20.465 178.185 3900 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.46 % Allowed : 10.07 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.75 (0.23), residues: 1368 helix: 1.25 (0.20), residues: 682 sheet: -0.15 (0.41), residues: 155 loop : -0.17 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1007 TYR 0.017 0.001 TYR A 767 PHE 0.019 0.001 PHE A 242 TRP 0.007 0.001 TRP A1035 HIS 0.005 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (15427) covalent geometry : angle 0.53053 / 0.30 (21619) hydrogen bonds : bond 0.04360 / 2.89 ( 721) hydrogen bonds : angle 4.35330 / 3.16 ( 1898) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: A 413 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8473 (ttp-170) REVERT: A 440 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: A 564 GLU cc_start: 0.8090 (tt0) cc_final: 0.7763 (tt0) REVERT: A 702 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 982 GLN cc_start: 0.7838 (pp30) cc_final: 0.7525 (pp30) outliers start: 18 outliers final: 9 residues processed: 67 average time/residue: 0.6688 time to fit residues: 49.8858 Evaluate side-chains 63 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1381 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 138 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.077937 restraints weight = 28345.821| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.25 r_work: 0.2974 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15427 Z= 0.231 Angle : 0.580 9.086 21619 Z= 0.320 Chirality : 0.042 0.354 2510 Planarity : 0.004 0.030 2136 Dihedral : 20.435 177.967 3900 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.87 % Allowed : 9.99 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.74 (0.23), residues: 1368 helix: 1.27 (0.20), residues: 682 sheet: -0.24 (0.41), residues: 158 loop : -0.18 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1007 TYR 0.016 0.002 TYR A 281 PHE 0.022 0.001 PHE A 242 TRP 0.009 0.001 TRP A1035 HIS 0.007 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (15427) covalent geometry : angle 0.57997 / 0.32 (21619) hydrogen bonds : bond 0.04556 / 3.03 ( 721) hydrogen bonds : angle 4.40151 / 3.19 ( 1898) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 413 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8525 (ttp-170) REVERT: A 440 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: A 564 GLU cc_start: 0.8193 (tt0) cc_final: 0.7904 (tt0) REVERT: A 691 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8772 (m) REVERT: A 702 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7638 (tm-30) REVERT: A 768 MET cc_start: 0.7526 (mtp) cc_final: 0.7157 (mtt) REVERT: A 910 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8492 (ttm170) REVERT: A 982 GLN cc_start: 0.7887 (pp30) cc_final: 0.7516 (pp30) outliers start: 23 outliers final: 10 residues processed: 72 average time/residue: 0.6190 time to fit residues: 49.5281 Evaluate side-chains 64 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1381 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 147 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.107032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.079147 restraints weight = 28240.951| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.27 r_work: 0.2999 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15427 Z= 0.173 Angle : 0.540 9.448 21619 Z= 0.303 Chirality : 0.040 0.358 2510 Planarity : 0.003 0.034 2136 Dihedral : 20.408 178.019 3900 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.87 % Allowed : 10.80 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.86 (0.23), residues: 1368 helix: 1.37 (0.20), residues: 683 sheet: -0.15 (0.42), residues: 153 loop : -0.15 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1198 TYR 0.015 0.001 TYR A 281 PHE 0.019 0.001 PHE A 242 TRP 0.006 0.001 TRP A1035 HIS 0.004 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (15427) covalent geometry : angle 0.53968 / 0.30 (21619) hydrogen bonds : bond 0.04341 / 2.88 ( 721) hydrogen bonds : angle 4.32439 / 3.14 ( 1898) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8511 (ttp-170) REVERT: A 440 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: A 564 GLU cc_start: 0.8123 (tt0) cc_final: 0.7903 (mt-10) REVERT: A 691 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8729 (m) REVERT: A 702 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 768 MET cc_start: 0.7574 (mtp) cc_final: 0.7223 (mtt) REVERT: A 910 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8291 (ttm170) REVERT: A 982 GLN cc_start: 0.7859 (pp30) cc_final: 0.7525 (pp30) REVERT: A 1288 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8305 (pm20) outliers start: 23 outliers final: 10 residues processed: 75 average time/residue: 0.6031 time to fit residues: 50.1364 Evaluate side-chains 69 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1288 GLN Chi-restraints excluded: chain A residue 1381 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 134 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 32 optimal weight: 0.0010 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 20 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.108670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.081099 restraints weight = 28588.288| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.28 r_work: 0.3040 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15427 Z= 0.117 Angle : 0.513 9.674 21619 Z= 0.290 Chirality : 0.038 0.360 2510 Planarity : 0.003 0.031 2136 Dihedral : 20.403 178.242 3900 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.71 % Allowed : 11.13 % Favored : 87.16 % 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: 1.02 (0.23), residues: 1368 helix: 1.52 (0.20), residues: 683 sheet: -0.14 (0.42), residues: 153 loop : -0.05 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1198 TYR 0.033 0.001 TYR A 767 PHE 0.025 0.001 PHE A 160 TRP 0.007 0.001 TRP A1214 HIS 0.004 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 (15427) covalent geometry : angle 0.51286 / 0.29 (21619) hydrogen bonds : bond 0.04099 / 2.73 ( 721) hydrogen bonds : angle 4.20699 / 3.05 ( 1898) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: A 564 GLU cc_start: 0.8047 (tt0) cc_final: 0.7752 (mm-30) REVERT: A 691 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8709 (m) REVERT: A 702 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7419 (tm-30) REVERT: A 767 TYR cc_start: 0.7801 (p90) cc_final: 0.7440 (p90) REVERT: A 768 MET cc_start: 0.7459 (mtp) cc_final: 0.7039 (mtt) REVERT: A 910 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8312 (ttm170) REVERT: A 982 GLN cc_start: 0.7932 (pp30) cc_final: 0.7572 (pp30) outliers start: 21 outliers final: 11 residues processed: 75 average time/residue: 0.6662 time to fit residues: 55.1449 Evaluate side-chains 70 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1381 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.107575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079949 restraints weight = 28480.985| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.26 r_work: 0.3016 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15427 Z= 0.160 Angle : 0.529 9.126 21619 Z= 0.295 Chirality : 0.039 0.358 2510 Planarity : 0.003 0.039 2136 Dihedral : 20.358 178.242 3900 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.46 % Allowed : 11.78 % 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: 1.12 (0.23), residues: 1368 helix: 1.57 (0.20), residues: 683 sheet: 0.11 (0.43), residues: 148 loop : -0.05 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1198 TYR 0.032 0.002 TYR A 767 PHE 0.019 0.001 PHE A 242 TRP 0.007 0.001 TRP A1035 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (15427) covalent geometry : angle 0.52883 / 0.30 (21619) hydrogen bonds : bond 0.04145 / 2.76 ( 721) hydrogen bonds : angle 4.22022 / 3.07 ( 1898) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6666 (tm130) REVERT: A 440 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: A 564 GLU cc_start: 0.8076 (tt0) cc_final: 0.7824 (mm-30) REVERT: A 691 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8718 (m) REVERT: A 702 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7420 (tm-30) REVERT: A 767 TYR cc_start: 0.7798 (p90) cc_final: 0.7414 (p90) REVERT: A 768 MET cc_start: 0.7469 (mtp) cc_final: 0.7009 (mtt) REVERT: A 910 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8288 (ttm170) REVERT: A 982 GLN cc_start: 0.7940 (pp30) cc_final: 0.7579 (pp30) outliers start: 18 outliers final: 11 residues processed: 71 average time/residue: 0.6116 time to fit residues: 48.5170 Evaluate side-chains 71 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1381 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.107971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.080475 restraints weight = 28432.357| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.26 r_work: 0.3046 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15427 Z= 0.143 Angle : 0.523 9.609 21619 Z= 0.292 Chirality : 0.039 0.360 2510 Planarity : 0.003 0.042 2136 Dihedral : 20.351 178.225 3900 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.38 % Allowed : 11.78 % Favored : 86.84 % 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: 1.16 (0.23), residues: 1368 helix: 1.60 (0.20), residues: 683 sheet: 0.11 (0.43), residues: 148 loop : -0.01 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1198 TYR 0.035 0.001 TYR A 767 PHE 0.025 0.001 PHE A 160 TRP 0.006 0.001 TRP A1214 HIS 0.004 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15427) covalent geometry : angle 0.52298 / 0.29 (21619) hydrogen bonds : bond 0.04045 / 2.69 ( 721) hydrogen bonds : angle 4.19082 / 3.05 ( 1898) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.6624 (tm130) REVERT: A 440 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: A 564 GLU cc_start: 0.8076 (tt0) cc_final: 0.7842 (mm-30) REVERT: A 691 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8715 (m) REVERT: A 702 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 767 TYR cc_start: 0.7752 (p90) cc_final: 0.7371 (p90) REVERT: A 768 MET cc_start: 0.7431 (mtp) cc_final: 0.6987 (mtt) REVERT: A 910 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8238 (ttm170) REVERT: A 982 GLN cc_start: 0.7935 (pp30) cc_final: 0.7567 (pp30) outliers start: 17 outliers final: 10 residues processed: 74 average time/residue: 0.6390 time to fit residues: 52.5096 Evaluate side-chains 69 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 68 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 86 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 572 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.106932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079223 restraints weight = 28522.435| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.27 r_work: 0.3001 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15427 Z= 0.183 Angle : 0.556 12.787 21619 Z= 0.305 Chirality : 0.040 0.358 2510 Planarity : 0.003 0.047 2136 Dihedral : 20.330 178.118 3900 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.38 % Allowed : 11.86 % 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: 1.14 (0.23), residues: 1368 helix: 1.59 (0.20), residues: 683 sheet: 0.12 (0.43), residues: 148 loop : -0.03 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1198 TYR 0.034 0.002 TYR A 767 PHE 0.020 0.001 PHE A 242 TRP 0.007 0.001 TRP A1035 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (15427) covalent geometry : angle 0.55641 / 0.31 (21619) hydrogen bonds : bond 0.04182 / 2.79 ( 721) hydrogen bonds : angle 4.23159 / 3.08 ( 1898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4515.78 seconds wall clock time: 77 minutes 59.09 seconds (4679.09 seconds total)