Starting phenix.real_space_refine on Sat Oct 11 12:42:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umf_42378/10_2025/8umf_42378.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umf_42378/10_2025/8umf_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 { model { file = "/net/cci-nas-00/data/ceres_data/8umf_42378/10_2025/8umf_42378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umf_42378/10_2025/8umf_42378.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8umf_42378/10_2025/8umf_42378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umf_42378/10_2025/8umf_42378.map" } 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-2.0-5842/lib/python3.9/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: 3.60, per 1000 atoms: 0.24 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: 1.23 Conformation dependent library (CDL) restraints added in 431.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.14 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: 3.90 Time building geometry restraints manager: 1.53 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=" C3' C B 57 " pdb=" O3' C B 57 " ideal model delta sigma weight residual 1.427 1.457 -0.030 1.50e-02 4.44e+03 3.87e+00 bond pdb=" CB ARG A 70 " pdb=" CG ARG A 70 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.65e+00 bond pdb=" CB VAL A1226 " pdb=" CG1 VAL A1226 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.35e+00 bond pdb=" CG LYS A 888 " pdb=" CD LYS A 888 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.10e+00 bond pdb=" CD LYS A 888 " pdb=" CE LYS A 888 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.02e+00 ... (remaining 15422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 20876 1.92 - 3.83: 624 3.83 - 5.75: 89 5.75 - 7.66: 22 7.66 - 9.58: 8 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 120.20 127.50 -7.30 1.50e+00 4.44e-01 2.37e+01 angle pdb=" C LYS A 679 " pdb=" N ASN A 680 " pdb=" CA ASN A 680 " ideal model delta sigma weight residual 122.46 128.25 -5.79 1.41e+00 5.03e-01 1.69e+01 angle pdb=" C ASN A 766 " pdb=" N TYR A 767 " pdb=" CA TYR A 767 " ideal model delta sigma weight residual 122.54 115.91 6.63 1.65e+00 3.67e-01 1.62e+01 angle pdb=" N GLU A 370 " pdb=" CA GLU A 370 " pdb=" C GLU A 370 " ideal model delta sigma weight residual 111.02 115.62 -4.60 1.22e+00 6.72e-01 1.42e+01 angle pdb=" N GLN A 158 " pdb=" CA GLN A 158 " pdb=" CB GLN A 158 " ideal model delta sigma weight residual 110.39 116.52 -6.13 1.66e+00 3.63e-01 1.36e+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: 2058 0.057 - 0.115: 380 0.115 - 0.172: 61 0.172 - 0.230: 9 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: 4.740 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.930 Find NCS groups from input model: 0.060 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 0.051 15427 Z= 0.232 Angle : 0.802 9.576 21619 Z= 0.436 Chirality : 0.047 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 aren 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 covalent geometry : bond 0.00506 (15427) covalent geometry : angle 0.80164 (21619) hydrogen bonds : bond 0.13890 ( 721) hydrogen bonds : angle 6.62360 ( 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 : 0.524 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 106 average time/residue: 0.7823 time to fit residues: 89.5836 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 : 0.492 ------------------------------------------------------------------------------- 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: 3.9990 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: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.106827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.079027 restraints weight = 28029.223| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.31 r_work: 0.2981 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15427 Z= 0.206 Angle : 0.601 7.184 21619 Z= 0.324 Chirality : 0.040 0.210 2510 Planarity : 0.004 0.035 2136 Dihedral : 20.565 177.917 3904 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.22 % Allowed : 6.01 % Favored : 92.77 % 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 aren not related in a simple way. whole: -0.10 (0.22), residues: 1368 helix: 0.41 (0.19), residues: 681 sheet: -0.25 (0.41), residues: 155 loop : -0.47 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 655 TYR 0.016 0.002 TYR A 767 PHE 0.023 0.001 PHE A 160 TRP 0.009 0.001 TRP A1035 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd covalent geometry : bond 0.00449 (15427) covalent geometry : angle 0.60142 (21619) hydrogen bonds : bond 0.04436 ( 721) hydrogen bonds : angle 4.76137 ( 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 79 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 158 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7990 (pm20) REVERT: A 413 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8526 (ttp-170) REVERT: A 440 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: A 702 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 982 GLN cc_start: 0.7808 (pp30) cc_final: 0.7548 (pp30) outliers start: 15 outliers final: 8 residues processed: 72 average time/residue: 0.6395 time to fit residues: 50.9828 Evaluate side-chains 64 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 457 ASP Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 691 SER 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: 2.9990 chunk 30 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3577 r_free = 0.3577 target = 0.106582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.078750 restraints weight = 28228.005| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.32 r_work: 0.2980 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15427 Z= 0.192 Angle : 0.570 7.606 21619 Z= 0.305 Chirality : 0.039 0.192 2510 Planarity : 0.003 0.030 2136 Dihedral : 20.532 177.606 3902 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.22 % Allowed : 8.69 % Favored : 90.09 % 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 aren not related in a simple way. whole: 0.37 (0.23), residues: 1368 helix: 0.87 (0.20), residues: 682 sheet: -0.21 (0.41), residues: 155 loop : -0.29 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 518 TYR 0.034 0.002 TYR A 767 PHE 0.019 0.001 PHE A 242 TRP 0.008 0.001 TRP A1035 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd covalent geometry : bond 0.00418 (15427) covalent geometry : angle 0.56999 (21619) hydrogen bonds : bond 0.04166 ( 721) hydrogen bonds : angle 4.49567 ( 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: 15 poor density : 62 time to evaluate : 0.546 Fit side-chains REVERT: A 158 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: A 413 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8503 (ttp-170) REVERT: A 440 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: A 702 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 982 GLN cc_start: 0.7854 (pp30) cc_final: 0.7554 (pp30) outliers start: 15 outliers final: 5 residues processed: 72 average time/residue: 0.6654 time to fit residues: 53.0269 Evaluate side-chains 59 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 765 MET 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: 2.9990 chunk 121 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 chunk 127 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 133 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3569 r_free = 0.3569 target = 0.106007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078393 restraints weight = 28164.327| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.29 r_work: 0.2976 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15427 Z= 0.197 Angle : 0.561 9.511 21619 Z= 0.299 Chirality : 0.039 0.190 2510 Planarity : 0.003 0.027 2136 Dihedral : 20.427 177.697 3900 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.30 % Allowed : 9.50 % Favored : 89.20 % 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 aren not related in a simple way. whole: 0.63 (0.23), residues: 1368 helix: 1.13 (0.20), residues: 682 sheet: -0.18 (0.41), residues: 155 loop : -0.19 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1007 TYR 0.033 0.001 TYR A 767 PHE 0.026 0.001 PHE A 160 TRP 0.007 0.001 TRP A1035 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd covalent geometry : bond 0.00433 (15427) covalent geometry : angle 0.56095 (21619) hydrogen bonds : bond 0.03988 ( 721) hydrogen bonds : angle 4.36874 ( 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 75 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.571 Fit side-chains REVERT: A 158 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: A 413 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8524 (ttp-170) REVERT: A 440 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: A 702 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 910 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8371 (ttm170) REVERT: A 982 GLN cc_start: 0.7913 (pp30) cc_final: 0.7572 (pp30) outliers start: 16 outliers final: 8 residues processed: 70 average time/residue: 0.6926 time to fit residues: 53.6295 Evaluate side-chains 61 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 767 TYR 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 1381 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 138 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1288 GLN ** 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 = 0.3560 r_free = 0.3560 target = 0.105429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077676 restraints weight = 28401.188| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.29 r_work: 0.2959 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15427 Z= 0.223 Angle : 0.570 8.090 21619 Z= 0.303 Chirality : 0.039 0.191 2510 Planarity : 0.003 0.028 2136 Dihedral : 20.402 177.651 3900 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.87 % Allowed : 9.75 % Favored : 88.38 % 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 aren not related in a simple way. whole: 0.70 (0.23), residues: 1368 helix: 1.20 (0.20), residues: 683 sheet: -0.19 (0.42), residues: 153 loop : -0.16 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1198 TYR 0.030 0.002 TYR A 767 PHE 0.021 0.001 PHE A 242 TRP 0.008 0.001 TRP A1035 HIS 0.005 0.001 HIS A1105 Details of bonding type rmsd covalent geometry : bond 0.00492 (15427) covalent geometry : angle 0.56998 (21619) hydrogen bonds : bond 0.04092 ( 721) hydrogen bonds : angle 4.35232 ( 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 81 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 158 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: A 413 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8420 (ttp-170) REVERT: A 440 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: A 702 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 910 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8363 (ttm170) REVERT: A 982 GLN cc_start: 0.7878 (pp30) cc_final: 0.7532 (pp30) REVERT: A 1288 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8261 (pm20) outliers start: 23 outliers final: 11 residues processed: 78 average time/residue: 0.6828 time to fit residues: 58.6474 Evaluate side-chains 70 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 288 LYS Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 688 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 138 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 chunk 16 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3551 r_free = 0.3551 target = 0.104902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077332 restraints weight = 28189.367| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.28 r_work: 0.2952 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15427 Z= 0.237 Angle : 0.578 9.673 21619 Z= 0.307 Chirality : 0.040 0.191 2510 Planarity : 0.003 0.027 2136 Dihedral : 20.391 177.608 3900 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.19 % Allowed : 10.24 % Favored : 87.57 % 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 aren not related in a simple way. whole: 0.76 (0.23), residues: 1368 helix: 1.25 (0.20), residues: 683 sheet: -0.17 (0.42), residues: 153 loop : -0.15 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1198 TYR 0.021 0.002 TYR A 819 PHE 0.021 0.001 PHE A 242 TRP 0.007 0.001 TRP A1035 HIS 0.006 0.001 HIS A1105 Details of bonding type rmsd covalent geometry : bond 0.00524 (15427) covalent geometry : angle 0.57820 (21619) hydrogen bonds : bond 0.04099 ( 721) hydrogen bonds : angle 4.35240 ( 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 83 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 158 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: A 201 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6770 (tm130) REVERT: A 413 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8455 (ttp-170) REVERT: A 440 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: A 702 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 768 MET cc_start: 0.7434 (ttm) cc_final: 0.7105 (mtp) REVERT: A 910 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8342 (ttm170) REVERT: A 982 GLN cc_start: 0.7896 (pp30) cc_final: 0.7535 (pp30) outliers start: 27 outliers final: 15 residues processed: 77 average time/residue: 0.6956 time to fit residues: 59.1089 Evaluate side-chains 78 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 201 GLN Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 413 ARG Chi-restraints excluded: chain A residue 437 HIS 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 763 LEU Chi-restraints excluded: chain A residue 767 TYR 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 1290 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: 0.7980 chunk 32 optimal weight: 0.0070 chunk 59 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3600 r_free = 0.3600 target = 0.107437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079863 restraints weight = 28445.055| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.26 r_work: 0.3017 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15427 Z= 0.140 Angle : 0.540 9.754 21619 Z= 0.286 Chirality : 0.037 0.193 2510 Planarity : 0.003 0.036 2136 Dihedral : 20.392 177.786 3900 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.03 % Allowed : 10.97 % Favored : 87.00 % 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 aren not related in a simple way. whole: 0.94 (0.23), residues: 1368 helix: 1.43 (0.20), residues: 683 sheet: -0.15 (0.42), residues: 153 loop : -0.07 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1198 TYR 0.020 0.001 TYR A 819 PHE 0.018 0.001 PHE A 242 TRP 0.007 0.001 TRP A1214 HIS 0.005 0.001 HIS A1406 Details of bonding type rmsd covalent geometry : bond 0.00302 (15427) covalent geometry : angle 0.53971 (21619) hydrogen bonds : bond 0.03804 ( 721) hydrogen bonds : angle 4.21596 ( 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 91 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 158 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: A 201 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6734 (tm130) REVERT: A 440 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: A 564 GLU cc_start: 0.8076 (tt0) cc_final: 0.7681 (mm-30) REVERT: A 702 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7478 (tm-30) REVERT: A 910 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8364 (ttm170) REVERT: A 982 GLN cc_start: 0.7964 (pp30) cc_final: 0.7604 (pp30) REVERT: A 1394 MET cc_start: 0.8368 (mpp) cc_final: 0.8168 (mpt) outliers start: 25 outliers final: 12 residues processed: 86 average time/residue: 0.6843 time to fit residues: 64.8169 Evaluate side-chains 75 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 231 GLU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 688 LEU 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 1290 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 32 optimal weight: 0.0970 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 96 optimal weight: 0.0060 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN A 748 ASN ** A1207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.110825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083754 restraints weight = 28773.680| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.28 r_work: 0.3109 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15427 Z= 0.106 Angle : 0.511 8.621 21619 Z= 0.272 Chirality : 0.036 0.193 2510 Planarity : 0.003 0.049 2136 Dihedral : 20.344 178.010 3900 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.87 % Allowed : 11.62 % Favored : 86.52 % 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 aren not related in a simple way. whole: 1.21 (0.23), residues: 1368 helix: 1.66 (0.20), residues: 684 sheet: 0.05 (0.42), residues: 148 loop : 0.02 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1198 TYR 0.040 0.001 TYR A 767 PHE 0.029 0.001 PHE A 160 TRP 0.006 0.001 TRP A1214 HIS 0.006 0.001 HIS A1406 Details of bonding type rmsd covalent geometry : bond 0.00220 (15427) covalent geometry : angle 0.51062 (21619) hydrogen bonds : bond 0.03445 ( 721) hydrogen bonds : angle 4.03614 ( 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 98 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 158 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: A 201 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.6378 (tm130) REVERT: A 231 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8320 (pm20) REVERT: A 440 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: A 564 GLU cc_start: 0.7998 (tt0) cc_final: 0.7571 (mm-30) REVERT: A 702 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7420 (tm-30) REVERT: A 982 GLN cc_start: 0.7989 (pp30) cc_final: 0.7605 (pp30) outliers start: 23 outliers final: 10 residues processed: 88 average time/residue: 0.6166 time to fit residues: 60.0646 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 : 0.507 ------------------------------------------------------------------------------- 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 231 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 763 LEU 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 1290 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 133 optimal weight: 0.1980 chunk 86 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.108287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080433 restraints weight = 28801.743| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.26 r_work: 0.2986 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2093 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= 0.233 Angle : 0.582 11.291 21619 Z= 0.306 Chirality : 0.039 0.219 2510 Planarity : 0.003 0.032 2136 Dihedral : 20.297 177.546 3900 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.71 % Allowed : 12.19 % Favored : 86.11 % 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 aren not related in a simple way. whole: 1.15 (0.23), residues: 1368 helix: 1.58 (0.20), residues: 681 sheet: 0.09 (0.43), residues: 150 loop : -0.00 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 392 TYR 0.016 0.002 TYR A 819 PHE 0.021 0.001 PHE A 242 TRP 0.008 0.001 TRP A1035 HIS 0.006 0.001 HIS A1105 Details of bonding type rmsd covalent geometry : bond 0.00519 (15427) covalent geometry : angle 0.58230 (21619) hydrogen bonds : bond 0.03878 ( 721) hydrogen bonds : angle 4.21440 ( 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 81 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 158 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: A 201 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6578 (tm130) REVERT: A 440 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: A 564 GLU cc_start: 0.8048 (tt0) cc_final: 0.7613 (tp30) REVERT: A 702 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 982 GLN cc_start: 0.7994 (pp30) cc_final: 0.7625 (pp30) outliers start: 21 outliers final: 10 residues processed: 77 average time/residue: 0.6668 time to fit residues: 56.7015 Evaluate side-chains 70 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 231 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 440 GLN 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 1290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 123 optimal weight: 0.0770 chunk 143 optimal weight: 4.9990 chunk 128 optimal weight: 0.3980 chunk 134 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3628 r_free = 0.3628 target = 0.109195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081992 restraints weight = 28548.272| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.27 r_work: 0.3073 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15427 Z= 0.125 Angle : 0.530 11.137 21619 Z= 0.280 Chirality : 0.036 0.232 2510 Planarity : 0.003 0.033 2136 Dihedral : 20.286 177.726 3900 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.30 % Allowed : 12.67 % Favored : 86.03 % 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 aren not related in a simple way. whole: 1.29 (0.23), residues: 1368 helix: 1.72 (0.20), residues: 683 sheet: 0.09 (0.43), residues: 150 loop : 0.05 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1198 TYR 0.032 0.001 TYR A 767 PHE 0.022 0.001 PHE A 160 TRP 0.007 0.001 TRP A 338 HIS 0.004 0.001 HIS A1406 Details of bonding type rmsd covalent geometry : bond 0.00269 (15427) covalent geometry : angle 0.52988 (21619) hydrogen bonds : bond 0.03517 ( 721) hydrogen bonds : angle 4.06196 ( 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 79 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 158 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: A 201 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.6486 (tm130) REVERT: A 231 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8324 (pm20) REVERT: A 440 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: A 540 TYR cc_start: 0.8657 (m-80) cc_final: 0.8008 (m-80) REVERT: A 564 GLU cc_start: 0.8004 (tt0) cc_final: 0.7559 (mm-30) REVERT: A 702 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7330 (tm-30) REVERT: A 982 GLN cc_start: 0.7949 (pp30) cc_final: 0.7578 (pp30) outliers start: 16 outliers final: 9 residues processed: 75 average time/residue: 0.5752 time to fit residues: 48.1907 Evaluate side-chains 74 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 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 231 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 440 GLN 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 1290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 68 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 0.2980 chunk 114 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.107067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079549 restraints weight = 28597.973| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.26 r_work: 0.3010 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15427 Z= 0.192 Angle : 0.556 10.483 21619 Z= 0.292 Chirality : 0.038 0.253 2510 Planarity : 0.003 0.029 2136 Dihedral : 20.207 177.490 3900 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.30 % Allowed : 12.84 % Favored : 85.87 % 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 aren not related in a simple way. whole: 1.24 (0.23), residues: 1368 helix: 1.67 (0.20), residues: 682 sheet: 0.15 (0.43), residues: 150 loop : 0.01 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1198 TYR 0.017 0.001 TYR A 819 PHE 0.020 0.001 PHE A 242 TRP 0.009 0.001 TRP A 139 HIS 0.007 0.001 HIS A1406 Details of bonding type rmsd covalent geometry : bond 0.00425 (15427) covalent geometry : angle 0.55630 (21619) hydrogen bonds : bond 0.03698 ( 721) hydrogen bonds : angle 4.13232 ( 1898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4959.92 seconds wall clock time: 85 minutes 28.40 seconds (5128.40 seconds total)