Starting phenix.real_space_refine on Sat Aug 23 15:45:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfl_40444/08_2025/8sfl_40444.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfl_40444/08_2025/8sfl_40444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sfl_40444/08_2025/8sfl_40444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfl_40444/08_2025/8sfl_40444.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sfl_40444/08_2025/8sfl_40444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfl_40444/08_2025/8sfl_40444.map" } resolution = 3.3 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 179 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 113 5.49 5 S 26 5.16 5 C 7912 2.51 5 N 2225 2.21 5 O 2695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12971 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1296, 10610 Classifications: {'peptide': 1296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1246} Chain breaks: 2 Chain: "B" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 721 Classifications: {'RNA': 34} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 15, 'rna3p_pyr': 13} Link IDs: {'rna2p': 6, 'rna3p': 27} Chain: "C" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 815 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "D" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 825 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Time building chain proxies: 3.45, per 1000 atoms: 0.27 Number of scatterers: 12971 At special positions: 0 Unit cell: (105.791, 102.459, 148.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 113 15.00 O 2695 8.00 N 2225 7.00 C 7912 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: 1.17 Conformation dependent library (CDL) restraints added in 517.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 11 sheets defined 53.5% alpha, 11.7% beta 46 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.521A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 35 through 67 removed outlier: 3.691A pdb=" N GLU A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.906A pdb=" N ILE A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 88 through 111 removed outlier: 3.989A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.274A pdb=" N PHE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.579A pdb=" N LEU A 137 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 215 removed outlier: 4.126A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 230 Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.983A pdb=" N ALA A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.543A pdb=" N SER A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.563A pdb=" N ASN A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 370 through 379 removed outlier: 3.603A pdb=" N CYS A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 404 through 417 removed outlier: 3.951A pdb=" N GLU A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 428 through 452 removed outlier: 4.377A pdb=" N SER A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.586A pdb=" N MET A 507 " --> pdb=" O ILE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 3.582A pdb=" N PHE A 513 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 removed outlier: 4.134A pdb=" N LYS A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 620 Processing helix chain 'A' and resid 639 through 647 removed outlier: 4.364A pdb=" N LEU A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 663 removed outlier: 3.846A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 728 through 738 Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.508A pdb=" N PHE A 750 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.713A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 819 through 831 removed outlier: 3.775A pdb=" N GLU A 825 " --> pdb=" O THR A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 940 through 957 removed outlier: 4.957A pdb=" N VAL A 952 " --> pdb=" O GLU A 948 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA A 953 " --> pdb=" O LYS A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 969 Processing helix chain 'A' and resid 971 through 987 removed outlier: 3.941A pdb=" N HIS A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1021 removed outlier: 3.818A pdb=" N PHE A1015 " --> pdb=" O VAL A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1026 removed outlier: 4.112A pdb=" N LEU A1026 " --> pdb=" O LEU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 4.011A pdb=" N THR A1087 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A1088 " --> pdb=" O TRP A1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1084 through 1088' Processing helix chain 'A' and resid 1090 through 1100 Processing helix chain 'A' and resid 1177 through 1190 removed outlier: 3.718A pdb=" N GLU A1188 " --> pdb=" O ALA A1184 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A1189 " --> pdb=" O LEU A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1196 Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 4.268A pdb=" N LYS A1202 " --> pdb=" O ASN A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1224 Processing helix chain 'A' and resid 1252 through 1254 No H-bonds generated for 'chain 'A' and resid 1252 through 1254' Processing helix chain 'A' and resid 1261 through 1284 Processing helix chain 'A' and resid 1294 through 1306 removed outlier: 3.716A pdb=" N ARG A1306 " --> pdb=" O ILE A1302 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 removed outlier: 4.263A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.182A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419 removed outlier: 4.124A pdb=" N ILE A 418 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE A 365 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA5, first strand: chain 'A' and resid 799 through 800 removed outlier: 3.683A pdb=" N ILE A 858 " --> pdb=" O HIS A 800 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 805 through 811 removed outlier: 6.037A pdb=" N ILE A 850 " --> pdb=" O ASN A 808 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.502A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N SER A 931 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE A 915 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 905 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLU A 993 " --> pdb=" O ILE A 905 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ILE A 907 " --> pdb=" O GLU A 993 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A1065 " --> pdb=" O LEU A 992 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1103 through 1106 removed outlier: 3.901A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AB1, first strand: chain 'A' and resid 1159 through 1164 removed outlier: 5.332A pdb=" N ARG A1172 " --> pdb=" O VAL A1163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1226 through 1229 removed outlier: 4.887A pdb=" N PHE A1249 " --> pdb=" O SER A1239 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 111 hydrogen bonds 218 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 1.58 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: 2622 1.33 - 1.45: 3692 1.45 - 1.57: 6910 1.57 - 1.70: 225 1.70 - 1.82: 44 Bond restraints: 13493 Sorted by residual: bond pdb=" C ARG A 313 " pdb=" N ASN A 314 " ideal model delta sigma weight residual 1.324 1.403 -0.078 2.56e-02 1.53e+03 9.36e+00 bond pdb=" N ASN A 314 " pdb=" CA ASN A 314 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.41e-02 5.03e+03 6.36e+00 bond pdb=" C GLU A 508 " pdb=" N PRO A 509 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.25e+00 bond pdb=" CB ASN A 630 " pdb=" CG ASN A 630 " ideal model delta sigma weight residual 1.516 1.568 -0.052 2.50e-02 1.60e+03 4.25e+00 bond pdb=" CB LYS A 796 " pdb=" CG LYS A 796 " ideal model delta sigma weight residual 1.520 1.579 -0.059 3.00e-02 1.11e+03 3.90e+00 ... (remaining 13488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 18609 4.89 - 9.79: 95 9.79 - 14.68: 27 14.68 - 19.58: 1 19.58 - 24.47: 1 Bond angle restraints: 18733 Sorted by residual: angle pdb=" O3' DG D 6 " pdb=" P DA D 7 " pdb=" OP1 DA D 7 " ideal model delta sigma weight residual 108.00 132.47 -24.47 3.00e+00 1.11e-01 6.66e+01 angle pdb=" C PRO A1066 " pdb=" N ALA A1067 " pdb=" CA ALA A1067 " ideal model delta sigma weight residual 119.78 126.61 -6.83 1.24e+00 6.50e-01 3.03e+01 angle pdb=" OP1 DA D 7 " pdb=" P DA D 7 " pdb=" OP2 DA D 7 " ideal model delta sigma weight residual 120.00 104.32 15.68 3.00e+00 1.11e-01 2.73e+01 angle pdb=" CA LYS A 796 " pdb=" CB LYS A 796 " pdb=" CG LYS A 796 " ideal model delta sigma weight residual 114.10 123.54 -9.44 2.00e+00 2.50e-01 2.23e+01 angle pdb=" CB LYS A 796 " pdb=" CG LYS A 796 " pdb=" CD LYS A 796 " ideal model delta sigma weight residual 111.30 121.94 -10.64 2.30e+00 1.89e-01 2.14e+01 ... (remaining 18728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 7294 34.81 - 69.63: 648 69.63 - 104.44: 23 104.44 - 139.25: 1 139.25 - 174.06: 6 Dihedral angle restraints: 7972 sinusoidal: 4143 harmonic: 3829 Sorted by residual: dihedral pdb=" O4' C B 11 " pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sinusoidal sigma weight residual 200.00 50.20 149.80 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 200.00 57.62 142.38 1 1.50e+01 4.44e-03 7.65e+01 dihedral pdb=" CA PHE A 323 " pdb=" C PHE A 323 " pdb=" N LYS A 324 " pdb=" CA LYS A 324 " ideal model delta harmonic sigma weight residual -180.00 -147.85 -32.15 0 5.00e+00 4.00e-02 4.13e+01 ... (remaining 7969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 2036 0.144 - 0.288: 33 0.288 - 0.431: 13 0.431 - 0.575: 2 0.575 - 0.719: 1 Chirality restraints: 2085 Sorted by residual: chirality pdb=" P DA D 7 " pdb=" OP1 DA D 7 " pdb=" OP2 DA D 7 " pdb=" O5' DA D 7 " both_signs ideal model delta sigma weight residual True 2.35 -3.06 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" P DG D 15 " pdb=" OP1 DG D 15 " pdb=" OP2 DG D 15 " pdb=" O5' DG D 15 " both_signs ideal model delta sigma weight residual True 2.35 -2.78 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" P DC C 26 " pdb=" OP1 DC C 26 " pdb=" OP2 DC C 26 " pdb=" O5' DC C 26 " both_signs ideal model delta sigma weight residual True 2.35 -2.78 -0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 2082 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 313 " 0.028 2.00e-02 2.50e+03 5.50e-02 3.02e+01 pdb=" C ARG A 313 " -0.095 2.00e-02 2.50e+03 pdb=" O ARG A 313 " 0.037 2.00e-02 2.50e+03 pdb=" N ASN A 314 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 528 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C VAL A 528 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL A 528 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 529 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 996 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.60e+00 pdb=" C ASN A 996 " -0.054 2.00e-02 2.50e+03 pdb=" O ASN A 996 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE A 997 " 0.018 2.00e-02 2.50e+03 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2312 2.77 - 3.30: 11841 3.30 - 3.83: 23376 3.83 - 4.37: 26478 4.37 - 4.90: 42980 Nonbonded interactions: 106987 Sorted by model distance: nonbonded pdb=" OG1 THR A 663 " pdb=" OD1 ASP A 665 " model vdw 2.236 3.040 nonbonded pdb=" OG SER A 839 " pdb=" OE1 GLU A 841 " model vdw 2.272 3.040 nonbonded pdb=" O2' U B 19 " pdb=" OP1 U B 21 " model vdw 2.299 3.040 nonbonded pdb=" ND2 ASN A 519 " pdb=" OP1 DC C 17 " model vdw 2.304 3.120 nonbonded pdb=" N ASP A 820 " pdb=" OD1 ASP A 820 " model vdw 2.339 3.120 ... (remaining 106982 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.030 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 0.078 13493 Z= 0.216 Angle : 1.004 24.474 18733 Z= 0.487 Chirality : 0.061 0.719 2085 Planarity : 0.006 0.063 1999 Dihedral : 21.889 174.063 5492 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.69 % Allowed : 23.92 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.87 (0.22), residues: 1290 helix: -0.63 (0.19), residues: 630 sheet: -0.12 (0.43), residues: 129 loop : -0.39 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 951 TYR 0.027 0.002 TYR A 829 PHE 0.048 0.002 PHE A1079 TRP 0.012 0.002 TRP A 958 HIS 0.011 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00487 (13493) covalent geometry : angle 1.00450 (18733) hydrogen bonds : bond 0.12839 ( 622) hydrogen bonds : angle 5.52241 ( 1682) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 83 average time/residue: 0.1293 time to fit residues: 15.8072 Evaluate side-chains 62 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 1091 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS A 534 ASN A 996 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.060902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.038239 restraints weight = 59134.282| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.96 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13493 Z= 0.164 Angle : 0.613 8.356 18733 Z= 0.325 Chirality : 0.040 0.181 2085 Planarity : 0.004 0.045 1999 Dihedral : 22.612 171.450 2814 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.15 % Allowed : 20.40 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.24), residues: 1290 helix: 0.66 (0.21), residues: 639 sheet: 0.03 (0.44), residues: 129 loop : 0.04 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 113 TYR 0.020 0.001 TYR A 764 PHE 0.015 0.001 PHE A 318 TRP 0.008 0.001 TRP A 73 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00361 (13493) covalent geometry : angle 0.61342 (18733) hydrogen bonds : bond 0.03593 ( 622) hydrogen bonds : angle 4.22844 ( 1682) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LEU cc_start: 0.9358 (tp) cc_final: 0.9113 (mt) REVERT: A 526 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: A 671 GLU cc_start: 0.9487 (OUTLIER) cc_final: 0.9223 (mm-30) REVERT: A 786 GLU cc_start: 0.7993 (mp0) cc_final: 0.7783 (mp0) REVERT: A 798 MET cc_start: 0.9172 (ttt) cc_final: 0.8713 (tmm) REVERT: A 969 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8510 (tp40) REVERT: A 1014 GLN cc_start: 0.9433 (tt0) cc_final: 0.8623 (tt0) REVERT: A 1018 MET cc_start: 0.9167 (mtm) cc_final: 0.8861 (mtm) REVERT: A 1055 MET cc_start: 0.8868 (ppp) cc_final: 0.8174 (ppp) outliers start: 25 outliers final: 6 residues processed: 78 average time/residue: 0.1097 time to fit residues: 13.3992 Evaluate side-chains 62 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1084 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1290 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.060049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.037033 restraints weight = 61627.431| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 4.00 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13493 Z= 0.185 Angle : 0.600 8.228 18733 Z= 0.315 Chirality : 0.040 0.256 2085 Planarity : 0.004 0.045 1999 Dihedral : 22.562 171.387 2808 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.93 % Allowed : 19.36 % Favored : 77.71 % 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: 1.05 (0.24), residues: 1290 helix: 1.31 (0.22), residues: 633 sheet: 0.06 (0.45), residues: 131 loop : 0.28 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 113 TYR 0.020 0.001 TYR A 764 PHE 0.012 0.001 PHE A 198 TRP 0.006 0.001 TRP A1258 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00403 (13493) covalent geometry : angle 0.59991 (18733) hydrogen bonds : bond 0.03479 ( 622) hydrogen bonds : angle 4.04071 ( 1682) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 56 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.8824 (p) REVERT: A 260 GLN cc_start: 0.9278 (pt0) cc_final: 0.8947 (pt0) REVERT: A 526 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: A 671 GLU cc_start: 0.9470 (OUTLIER) cc_final: 0.9194 (mm-30) REVERT: A 786 GLU cc_start: 0.8111 (mp0) cc_final: 0.7895 (mp0) REVERT: A 798 MET cc_start: 0.9158 (ttt) cc_final: 0.8695 (tmm) REVERT: A 836 HIS cc_start: 0.8572 (m90) cc_final: 0.8364 (m90) REVERT: A 969 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8822 (tm-30) REVERT: A 1008 GLU cc_start: 0.8938 (mp0) cc_final: 0.8367 (mp0) REVERT: A 1055 MET cc_start: 0.9035 (ppp) cc_final: 0.8199 (ppp) outliers start: 34 outliers final: 15 residues processed: 84 average time/residue: 0.1156 time to fit residues: 14.8006 Evaluate side-chains 69 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1168 ARG Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 83 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 chunk 23 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.0170 chunk 108 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.060497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.038079 restraints weight = 59505.822| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.86 r_work: 0.2482 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13493 Z= 0.120 Angle : 0.570 9.849 18733 Z= 0.299 Chirality : 0.039 0.272 2085 Planarity : 0.003 0.044 1999 Dihedral : 22.480 169.435 2808 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.50 % Allowed : 20.22 % Favored : 77.28 % 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: 1.18 (0.25), residues: 1290 helix: 1.42 (0.22), residues: 633 sheet: 0.16 (0.45), residues: 130 loop : 0.31 (0.29), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1003 TYR 0.017 0.001 TYR A 764 PHE 0.017 0.001 PHE A 323 TRP 0.008 0.001 TRP A 958 HIS 0.005 0.000 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00262 (13493) covalent geometry : angle 0.57049 (18733) hydrogen bonds : bond 0.03118 ( 622) hydrogen bonds : angle 3.89727 ( 1682) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9279 (pt0) cc_final: 0.8977 (pt0) REVERT: A 526 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: A 671 GLU cc_start: 0.9627 (OUTLIER) cc_final: 0.9382 (mm-30) REVERT: A 798 MET cc_start: 0.9290 (ttt) cc_final: 0.8833 (tmm) REVERT: A 836 HIS cc_start: 0.8815 (m90) cc_final: 0.8582 (m90) REVERT: A 969 GLN cc_start: 0.9390 (tm-30) cc_final: 0.9054 (tm-30) REVERT: A 1008 GLU cc_start: 0.9166 (mp0) cc_final: 0.8614 (mp0) REVERT: A 1055 MET cc_start: 0.9039 (ppp) cc_final: 0.8370 (ppp) REVERT: A 1062 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9111 (tt) REVERT: A 1260 MET cc_start: 0.9112 (mmm) cc_final: 0.8790 (mmm) outliers start: 29 outliers final: 15 residues processed: 83 average time/residue: 0.1153 time to fit residues: 14.5285 Evaluate side-chains 71 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1168 ARG Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.058593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.036104 restraints weight = 61173.533| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 3.82 r_work: 0.2448 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13493 Z= 0.217 Angle : 0.605 9.665 18733 Z= 0.319 Chirality : 0.040 0.287 2085 Planarity : 0.003 0.045 1999 Dihedral : 22.539 170.477 2808 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.18 % Allowed : 20.57 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.35 (0.25), residues: 1290 helix: 1.62 (0.22), residues: 632 sheet: -0.09 (0.44), residues: 134 loop : 0.42 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 790 TYR 0.029 0.001 TYR A 764 PHE 0.017 0.001 PHE A 323 TRP 0.006 0.001 TRP A 958 HIS 0.005 0.001 HIS A1269 Details of bonding type rmsd covalent geometry : bond 0.00469 (13493) covalent geometry : angle 0.60529 (18733) hydrogen bonds : bond 0.03539 ( 622) hydrogen bonds : angle 3.94199 ( 1682) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 51 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9324 (pt0) cc_final: 0.9013 (pt0) REVERT: A 671 GLU cc_start: 0.9613 (OUTLIER) cc_final: 0.9386 (mp0) REVERT: A 798 MET cc_start: 0.9282 (ttt) cc_final: 0.8853 (tmm) REVERT: A 836 HIS cc_start: 0.8851 (m90) cc_final: 0.8589 (m90) REVERT: A 969 GLN cc_start: 0.9421 (tm-30) cc_final: 0.9195 (tm-30) REVERT: A 1055 MET cc_start: 0.9129 (ppp) cc_final: 0.8151 (ppp) REVERT: A 1062 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9106 (tt) REVERT: A 1081 ASP cc_start: 0.9217 (t0) cc_final: 0.8730 (t0) outliers start: 37 outliers final: 27 residues processed: 83 average time/residue: 0.1116 time to fit residues: 14.4304 Evaluate side-chains 76 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 47 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 575 TYR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1168 ARG Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 101 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 120 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 1 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: A1143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.059407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.036978 restraints weight = 60230.619| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 3.83 r_work: 0.2480 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13493 Z= 0.140 Angle : 0.569 10.430 18733 Z= 0.298 Chirality : 0.039 0.298 2085 Planarity : 0.003 0.045 1999 Dihedral : 22.497 170.336 2808 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.18 % Allowed : 20.83 % Favored : 75.99 % 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: 1.43 (0.25), residues: 1290 helix: 1.64 (0.22), residues: 637 sheet: 0.01 (0.45), residues: 135 loop : 0.50 (0.30), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 951 TYR 0.025 0.001 TYR A 764 PHE 0.011 0.001 PHE A 323 TRP 0.007 0.001 TRP A 958 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00307 (13493) covalent geometry : angle 0.56880 (18733) hydrogen bonds : bond 0.03127 ( 622) hydrogen bonds : angle 3.82463 ( 1682) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 54 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9322 (pt0) cc_final: 0.9009 (pt0) REVERT: A 671 GLU cc_start: 0.9602 (OUTLIER) cc_final: 0.9372 (mp0) REVERT: A 836 HIS cc_start: 0.8836 (m90) cc_final: 0.8565 (m90) REVERT: A 955 ARG cc_start: 0.9532 (tpp80) cc_final: 0.9189 (tpt90) REVERT: A 1014 GLN cc_start: 0.9494 (tt0) cc_final: 0.9175 (tt0) REVERT: A 1055 MET cc_start: 0.9065 (ppp) cc_final: 0.8209 (ppp) REVERT: A 1062 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9065 (tt) REVERT: A 1081 ASP cc_start: 0.9164 (t0) cc_final: 0.8916 (t0) REVERT: A 1260 MET cc_start: 0.9082 (mmm) cc_final: 0.8712 (mmm) outliers start: 37 outliers final: 29 residues processed: 86 average time/residue: 0.1124 time to fit residues: 14.9784 Evaluate side-chains 80 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 49 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1168 ARG Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 52 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 120 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3370 r_free = 0.3370 target = 0.059436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.037035 restraints weight = 60400.841| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.84 r_work: 0.2488 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13493 Z= 0.134 Angle : 0.568 10.747 18733 Z= 0.296 Chirality : 0.039 0.319 2085 Planarity : 0.003 0.045 1999 Dihedral : 22.434 171.140 2808 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.18 % Allowed : 20.91 % Favored : 75.90 % 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: 1.51 (0.25), residues: 1290 helix: 1.72 (0.22), residues: 637 sheet: -0.03 (0.44), residues: 138 loop : 0.54 (0.30), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 955 TYR 0.023 0.001 TYR A 764 PHE 0.012 0.001 PHE A 165 TRP 0.007 0.001 TRP A 958 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00295 (13493) covalent geometry : angle 0.56764 (18733) hydrogen bonds : bond 0.03049 ( 622) hydrogen bonds : angle 3.75365 ( 1682) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 57 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9314 (pt0) cc_final: 0.9011 (pt0) REVERT: A 671 GLU cc_start: 0.9597 (OUTLIER) cc_final: 0.9367 (mp0) REVERT: A 836 HIS cc_start: 0.8819 (m90) cc_final: 0.8533 (m90) REVERT: A 955 ARG cc_start: 0.9525 (tpp80) cc_final: 0.9192 (tpt90) REVERT: A 1055 MET cc_start: 0.9085 (ppp) cc_final: 0.8401 (ppp) REVERT: A 1062 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9071 (tt) REVERT: A 1081 ASP cc_start: 0.9163 (t0) cc_final: 0.8946 (t0) REVERT: A 1260 MET cc_start: 0.9119 (mmm) cc_final: 0.8788 (mmm) outliers start: 37 outliers final: 31 residues processed: 88 average time/residue: 0.1065 time to fit residues: 14.4444 Evaluate side-chains 87 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 54 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 537 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1168 ARG Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 11 optimal weight: 9.9990 chunk 99 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.059187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.036867 restraints weight = 59915.742| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 3.80 r_work: 0.2484 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13493 Z= 0.144 Angle : 0.582 11.182 18733 Z= 0.299 Chirality : 0.039 0.315 2085 Planarity : 0.003 0.046 1999 Dihedral : 22.415 171.804 2808 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.36 % Allowed : 20.91 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.25), residues: 1290 helix: 1.78 (0.22), residues: 637 sheet: -0.00 (0.44), residues: 138 loop : 0.56 (0.30), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.022 0.001 TYR A 764 PHE 0.015 0.001 PHE A 165 TRP 0.010 0.001 TRP A 73 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00317 (13493) covalent geometry : angle 0.58164 (18733) hydrogen bonds : bond 0.03061 ( 622) hydrogen bonds : angle 3.73839 ( 1682) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 53 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.8818 (t80) REVERT: A 260 GLN cc_start: 0.9320 (pt0) cc_final: 0.9012 (pt0) REVERT: A 671 GLU cc_start: 0.9596 (OUTLIER) cc_final: 0.9364 (mp0) REVERT: A 836 HIS cc_start: 0.8819 (m90) cc_final: 0.8530 (m90) REVERT: A 955 ARG cc_start: 0.9538 (tpp80) cc_final: 0.9217 (tpt90) REVERT: A 969 GLN cc_start: 0.9380 (tp40) cc_final: 0.9155 (tp40) REVERT: A 1014 GLN cc_start: 0.9508 (tt0) cc_final: 0.8939 (tm-30) REVERT: A 1055 MET cc_start: 0.9049 (ppp) cc_final: 0.8498 (ppp) REVERT: A 1062 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9088 (tt) REVERT: A 1081 ASP cc_start: 0.9152 (t0) cc_final: 0.8950 (t0) REVERT: A 1260 MET cc_start: 0.9132 (mmm) cc_final: 0.8806 (mmm) outliers start: 39 outliers final: 32 residues processed: 86 average time/residue: 0.1063 time to fit residues: 14.2023 Evaluate side-chains 87 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1168 ARG Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1225 MET Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 136 optimal weight: 7.9990 chunk 103 optimal weight: 0.0970 chunk 99 optimal weight: 0.3980 chunk 49 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.059930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.037661 restraints weight = 60031.725| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.83 r_work: 0.2514 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13493 Z= 0.119 Angle : 0.572 11.499 18733 Z= 0.294 Chirality : 0.039 0.319 2085 Planarity : 0.003 0.046 1999 Dihedral : 22.340 172.226 2808 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.93 % Allowed : 21.51 % Favored : 75.56 % 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: 1.62 (0.25), residues: 1290 helix: 1.81 (0.22), residues: 636 sheet: 0.07 (0.45), residues: 138 loop : 0.59 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 955 TYR 0.021 0.001 TYR A 764 PHE 0.012 0.001 PHE A 165 TRP 0.008 0.001 TRP A 958 HIS 0.004 0.000 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00262 (13493) covalent geometry : angle 0.57225 (18733) hydrogen bonds : bond 0.02894 ( 622) hydrogen bonds : angle 3.67444 ( 1682) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 59 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9321 (pt0) cc_final: 0.9024 (pt0) REVERT: A 671 GLU cc_start: 0.9575 (OUTLIER) cc_final: 0.9342 (mp0) REVERT: A 836 HIS cc_start: 0.8780 (m90) cc_final: 0.8484 (m90) REVERT: A 879 TYR cc_start: 0.9445 (t80) cc_final: 0.8854 (t80) REVERT: A 955 ARG cc_start: 0.9521 (tpp80) cc_final: 0.9226 (tpt90) REVERT: A 969 GLN cc_start: 0.9437 (tp40) cc_final: 0.8692 (tp40) REVERT: A 1014 GLN cc_start: 0.9510 (tt0) cc_final: 0.8925 (tm-30) REVERT: A 1018 MET cc_start: 0.9582 (mmm) cc_final: 0.9164 (mtm) REVERT: A 1055 MET cc_start: 0.9051 (ppp) cc_final: 0.8542 (ppp) REVERT: A 1062 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9144 (tt) REVERT: A 1081 ASP cc_start: 0.9119 (t0) cc_final: 0.8917 (t0) REVERT: A 1260 MET cc_start: 0.9147 (mmm) cc_final: 0.8840 (mmm) outliers start: 34 outliers final: 29 residues processed: 85 average time/residue: 0.1190 time to fit residues: 15.2488 Evaluate side-chains 89 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1168 ARG Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 67 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 800 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.057816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.035254 restraints weight = 62561.736| |-----------------------------------------------------------------------------| r_work (start): 0.2588 rms_B_bonded: 3.82 r_work: 0.2420 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13493 Z= 0.253 Angle : 0.639 11.252 18733 Z= 0.334 Chirality : 0.041 0.331 2085 Planarity : 0.004 0.047 1999 Dihedral : 22.529 173.417 2808 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.93 % Allowed : 21.60 % Favored : 75.47 % 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: 1.67 (0.25), residues: 1290 helix: 1.88 (0.22), residues: 633 sheet: -0.03 (0.45), residues: 138 loop : 0.63 (0.30), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 43 TYR 0.020 0.002 TYR A 764 PHE 0.021 0.002 PHE A 165 TRP 0.010 0.002 TRP A 544 HIS 0.005 0.001 HIS A1269 Details of bonding type rmsd covalent geometry : bond 0.00546 (13493) covalent geometry : angle 0.63894 (18733) hydrogen bonds : bond 0.03714 ( 622) hydrogen bonds : angle 3.88925 ( 1682) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 51 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8832 (t80) REVERT: A 260 GLN cc_start: 0.9367 (pt0) cc_final: 0.9049 (pt0) REVERT: A 671 GLU cc_start: 0.9605 (OUTLIER) cc_final: 0.9378 (mp0) REVERT: A 798 MET cc_start: 0.9296 (ttt) cc_final: 0.8888 (tmm) REVERT: A 836 HIS cc_start: 0.8846 (m90) cc_final: 0.8559 (m-70) REVERT: A 969 GLN cc_start: 0.9505 (tp40) cc_final: 0.9255 (tm-30) REVERT: A 1014 GLN cc_start: 0.9543 (tt0) cc_final: 0.9007 (tm-30) REVERT: A 1055 MET cc_start: 0.9044 (ppp) cc_final: 0.8293 (ppp) REVERT: A 1062 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9087 (tt) outliers start: 34 outliers final: 30 residues processed: 81 average time/residue: 0.1119 time to fit residues: 14.0571 Evaluate side-chains 82 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 49 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1168 ARG Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.058427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.035895 restraints weight = 61701.612| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 3.81 r_work: 0.2443 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13493 Z= 0.186 Angle : 0.603 11.279 18733 Z= 0.312 Chirality : 0.040 0.316 2085 Planarity : 0.003 0.046 1999 Dihedral : 22.510 172.677 2808 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.27 % Allowed : 21.17 % Favored : 75.56 % 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: 1.71 (0.25), residues: 1290 helix: 1.89 (0.22), residues: 634 sheet: 0.01 (0.45), residues: 138 loop : 0.68 (0.30), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 210 TYR 0.019 0.001 TYR A 764 PHE 0.016 0.001 PHE A 165 TRP 0.008 0.001 TRP A 73 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00408 (13493) covalent geometry : angle 0.60268 (18733) hydrogen bonds : bond 0.03303 ( 622) hydrogen bonds : angle 3.82217 ( 1682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3210.85 seconds wall clock time: 56 minutes 7.09 seconds (3367.09 seconds total)