Starting phenix.real_space_refine on Thu Jul 31 04:05:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfl_40444/07_2025/8sfl_40444.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfl_40444/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfl_40444/07_2025/8sfl_40444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfl_40444/07_2025/8sfl_40444.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfl_40444/07_2025/8sfl_40444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfl_40444/07_2025/8sfl_40444.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.24, per 1000 atoms: 0.64 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: 3.16 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 5.32 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: 6.36 Time building geometry restraints manager: 3.84 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 38.120 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.570 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (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 TRP 0.012 0.002 TRP A 958 HIS 0.011 0.001 HIS A 415 PHE 0.048 0.002 PHE A1079 TYR 0.027 0.002 TYR A 829 ARG 0.011 0.001 ARG A 951 Details of bonding type rmsd hydrogen bonds : bond 0.12839 ( 622) hydrogen bonds : angle 5.52241 ( 1682) covalent geometry : bond 0.00487 (13493) covalent geometry : angle 1.00450 (18733) *********************** 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 : 1.323 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: 0.3075 time to fit residues: 38.2903 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 : 1.362 ------------------------------------------------------------------------------- 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 118 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 0.3980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS A 534 ASN A 744 GLN A 996 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.061526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.038859 restraints weight = 58814.003| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 3.98 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13493 Z= 0.143 Angle : 0.609 8.806 18733 Z= 0.323 Chirality : 0.039 0.190 2085 Planarity : 0.004 0.046 1999 Dihedral : 22.583 171.282 2814 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.98 % Allowed : 20.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1290 helix: 0.58 (0.21), residues: 639 sheet: 0.02 (0.43), residues: 129 loop : 0.01 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 73 HIS 0.006 0.001 HIS A 415 PHE 0.014 0.001 PHE A 318 TYR 0.019 0.001 TYR A 764 ARG 0.007 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 622) hydrogen bonds : angle 4.24885 ( 1682) covalent geometry : bond 0.00312 (13493) covalent geometry : angle 0.60938 (18733) *********************** 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 84 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9282 (pt0) cc_final: 0.9008 (pt0) REVERT: A 526 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: A 671 GLU cc_start: 0.9490 (OUTLIER) cc_final: 0.9223 (mm-30) REVERT: A 798 MET cc_start: 0.9162 (ttt) cc_final: 0.8695 (tmm) REVERT: A 969 GLN cc_start: 0.9164 (tm-30) cc_final: 0.8552 (tp40) REVERT: A 1014 GLN cc_start: 0.9435 (tt0) cc_final: 0.8560 (tt0) REVERT: A 1055 MET cc_start: 0.8836 (ppp) cc_final: 0.8316 (ppp) outliers start: 23 outliers final: 5 residues processed: 79 average time/residue: 0.2352 time to fit residues: 29.0394 Evaluate side-chains 63 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain A residue 165 PHE 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 671 GLU Chi-restraints excluded: chain A residue 982 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 61 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 115 optimal weight: 0.0470 overall best weight: 1.4682 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.061073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.038343 restraints weight = 59409.925| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.95 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1426 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 : 0.588 9.115 18733 Z= 0.306 Chirality : 0.039 0.269 2085 Planarity : 0.004 0.044 1999 Dihedral : 22.498 170.838 2808 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.24 % Allowed : 19.88 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1290 helix: 1.15 (0.21), residues: 639 sheet: 0.03 (0.45), residues: 131 loop : 0.25 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 958 HIS 0.005 0.001 HIS A 415 PHE 0.010 0.001 PHE A 318 TYR 0.020 0.001 TYR A 764 ARG 0.008 0.000 ARG A1003 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 622) hydrogen bonds : angle 4.00886 ( 1682) covalent geometry : bond 0.00315 (13493) covalent geometry : angle 0.58781 (18733) *********************** 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 88 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.9250 (pt0) cc_final: 0.8928 (pt0) REVERT: A 526 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: A 671 GLU cc_start: 0.9474 (OUTLIER) cc_final: 0.9185 (mm-30) REVERT: A 786 GLU cc_start: 0.8059 (mp0) cc_final: 0.7841 (mp0) REVERT: A 798 MET cc_start: 0.9164 (ttt) cc_final: 0.8698 (tmm) REVERT: A 836 HIS cc_start: 0.8510 (m90) cc_final: 0.8309 (m90) REVERT: A 969 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8765 (tm-30) REVERT: A 1008 GLU cc_start: 0.8916 (mp0) cc_final: 0.8342 (mp0) REVERT: A 1055 MET cc_start: 0.8978 (ppp) cc_final: 0.8422 (ppp) outliers start: 26 outliers final: 11 residues processed: 82 average time/residue: 0.2392 time to fit residues: 30.2337 Evaluate side-chains 69 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 303 ILE 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 1305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 58 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 91 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.061684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.039060 restraints weight = 59963.886| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 3.99 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 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 : 0.002 0.046 13493 Z= 0.115 Angle : 0.564 9.884 18733 Z= 0.294 Chirality : 0.039 0.259 2085 Planarity : 0.003 0.044 1999 Dihedral : 22.413 169.856 2808 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.67 % Allowed : 19.54 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1290 helix: 1.32 (0.22), residues: 639 sheet: 0.19 (0.45), residues: 130 loop : 0.30 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 958 HIS 0.005 0.000 HIS A 415 PHE 0.018 0.001 PHE A 323 TYR 0.021 0.001 TYR A 764 ARG 0.002 0.000 ARG A 951 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 622) hydrogen bonds : angle 3.86020 ( 1682) covalent geometry : bond 0.00250 (13493) covalent geometry : angle 0.56360 (18733) *********************** 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 96 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.8838 (p) REVERT: A 260 GLN cc_start: 0.9238 (pt0) cc_final: 0.8933 (pt0) REVERT: A 526 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: A 671 GLU cc_start: 0.9433 (OUTLIER) cc_final: 0.9171 (mp0) REVERT: A 798 MET cc_start: 0.9155 (ttt) cc_final: 0.8713 (tmm) REVERT: A 836 HIS cc_start: 0.8575 (m90) cc_final: 0.8343 (m90) REVERT: A 879 TYR cc_start: 0.9158 (t80) cc_final: 0.8801 (t80) REVERT: A 969 GLN cc_start: 0.9173 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 1055 MET cc_start: 0.9023 (ppp) cc_final: 0.8580 (ppp) REVERT: A 1062 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8903 (tt) REVERT: A 1260 MET cc_start: 0.9089 (mmm) cc_final: 0.8728 (mmm) outliers start: 31 outliers final: 14 residues processed: 89 average time/residue: 0.2362 time to fit residues: 32.6200 Evaluate side-chains 78 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 303 ILE Chi-restraints excluded: chain A residue 373 THR 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 546 VAL Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 960 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 12 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.056961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.034025 restraints weight = 62982.608| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 3.93 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 13493 Z= 0.421 Angle : 0.769 8.940 18733 Z= 0.404 Chirality : 0.045 0.304 2085 Planarity : 0.004 0.046 1999 Dihedral : 22.759 171.918 2808 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.61 % Allowed : 19.97 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1290 helix: 1.28 (0.21), residues: 636 sheet: -0.20 (0.45), residues: 134 loop : 0.25 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 483 HIS 0.009 0.002 HIS A1269 PHE 0.027 0.002 PHE A 323 TYR 0.031 0.002 TYR A 764 ARG 0.003 0.001 ARG A1306 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 622) hydrogen bonds : angle 4.32041 ( 1682) covalent geometry : bond 0.00893 (13493) covalent geometry : angle 0.76910 (18733) *********************** 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 87 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 45 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.9540 (OUTLIER) cc_final: 0.9042 (t80) REVERT: A 671 GLU cc_start: 0.9406 (OUTLIER) cc_final: 0.9149 (mm-30) REVERT: A 786 GLU cc_start: 0.8318 (mp0) cc_final: 0.7806 (mp0) REVERT: A 836 HIS cc_start: 0.8638 (m90) cc_final: 0.8391 (m90) REVERT: A 969 GLN cc_start: 0.9302 (tm-30) cc_final: 0.8975 (tm-30) REVERT: A 1055 MET cc_start: 0.9153 (ppp) cc_final: 0.7933 (ppp) REVERT: A 1062 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8915 (tt) REVERT: A 1081 ASP cc_start: 0.9192 (t0) cc_final: 0.8981 (t0) outliers start: 42 outliers final: 26 residues processed: 81 average time/residue: 0.2259 time to fit residues: 29.7085 Evaluate side-chains 72 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 43 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 152 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 310 LEU Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 420 LEU 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 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 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 1170 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1299 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 29 optimal weight: 0.0010 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1143 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 = 0.3346 r_free = 0.3346 target = 0.058520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.036012 restraints weight = 60833.110| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 3.84 r_work: 0.2451 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13493 Z= 0.152 Angle : 0.594 10.993 18733 Z= 0.309 Chirality : 0.040 0.289 2085 Planarity : 0.003 0.044 1999 Dihedral : 22.648 168.460 2808 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.41 % Allowed : 21.26 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1290 helix: 1.59 (0.21), residues: 637 sheet: -0.03 (0.45), residues: 133 loop : 0.43 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 958 HIS 0.004 0.001 HIS A 415 PHE 0.012 0.001 PHE A1049 TYR 0.026 0.001 TYR A 764 ARG 0.002 0.000 ARG A 951 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 622) hydrogen bonds : angle 3.94585 ( 1682) covalent geometry : bond 0.00334 (13493) covalent geometry : angle 0.59412 (18733) *********************** 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 76 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 48 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.9544 (OUTLIER) cc_final: 0.9111 (t80) REVERT: A 260 GLN cc_start: 0.9343 (pt0) cc_final: 0.9029 (pt0) REVERT: A 458 LEU cc_start: 0.9370 (tp) cc_final: 0.9148 (mt) REVERT: A 526 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.8030 (m-80) REVERT: A 671 GLU cc_start: 0.9602 (OUTLIER) cc_final: 0.9367 (mp0) REVERT: A 786 GLU cc_start: 0.8634 (mp0) cc_final: 0.8375 (mp0) REVERT: A 836 HIS cc_start: 0.8882 (m90) cc_final: 0.8621 (m90) REVERT: A 969 GLN cc_start: 0.9406 (tm-30) cc_final: 0.9185 (tm-30) REVERT: A 1008 GLU cc_start: 0.9300 (mp0) cc_final: 0.8827 (mp0) REVERT: A 1014 GLN cc_start: 0.9539 (tt0) cc_final: 0.9137 (tt0) REVERT: A 1055 MET cc_start: 0.9114 (ppp) cc_final: 0.8024 (ppp) REVERT: A 1062 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9168 (tt) REVERT: A 1081 ASP cc_start: 0.9187 (t0) cc_final: 0.8970 (t0) outliers start: 28 outliers final: 21 residues processed: 71 average time/residue: 0.2209 time to fit residues: 26.4312 Evaluate side-chains 72 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 420 LEU 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 671 GLU Chi-restraints excluded: chain A residue 873 VAL 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 1084 VAL Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1248 CYS 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 110 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 overall best weight: 3.2588 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.057568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.035108 restraints weight = 61195.968| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 3.78 r_work: 0.2417 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13493 Z= 0.242 Angle : 0.623 10.369 18733 Z= 0.326 Chirality : 0.041 0.314 2085 Planarity : 0.003 0.046 1999 Dihedral : 22.641 169.730 2808 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.93 % Allowed : 20.91 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1290 helix: 1.67 (0.22), residues: 636 sheet: -0.16 (0.45), residues: 138 loop : 0.47 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 958 HIS 0.005 0.001 HIS A1269 PHE 0.014 0.001 PHE A 323 TYR 0.024 0.001 TYR A 764 ARG 0.002 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 622) hydrogen bonds : angle 3.97962 ( 1682) covalent geometry : bond 0.00522 (13493) covalent geometry : angle 0.62324 (18733) *********************** 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 81 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 47 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.9544 (OUTLIER) cc_final: 0.9101 (t80) REVERT: A 260 GLN cc_start: 0.9364 (pt0) cc_final: 0.9042 (pt0) REVERT: A 526 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: A 671 GLU cc_start: 0.9594 (OUTLIER) cc_final: 0.9341 (mp0) REVERT: A 786 GLU cc_start: 0.8643 (mp0) cc_final: 0.8368 (mp0) REVERT: A 798 MET cc_start: 0.9290 (ttt) cc_final: 0.8868 (tmm) REVERT: A 836 HIS cc_start: 0.8864 (m90) cc_final: 0.8584 (m90) REVERT: A 969 GLN cc_start: 0.9437 (tm-30) cc_final: 0.9231 (tm-30) REVERT: A 1014 GLN cc_start: 0.9572 (tt0) cc_final: 0.9317 (tt0) REVERT: A 1055 MET cc_start: 0.9125 (ppp) cc_final: 0.7913 (ppp) REVERT: A 1062 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9144 (tt) outliers start: 34 outliers final: 27 residues processed: 75 average time/residue: 0.2150 time to fit residues: 26.3312 Evaluate side-chains 77 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 46 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 165 PHE 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 368 HIS Chi-restraints excluded: chain A residue 420 LEU 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 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 1091 HIS Chi-restraints excluded: chain A residue 1119 MET 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 115 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.058364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.035880 restraints weight = 60976.409| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 3.82 r_work: 0.2447 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2495 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= 0.169 Angle : 0.588 10.788 18733 Z= 0.307 Chirality : 0.040 0.296 2085 Planarity : 0.003 0.045 1999 Dihedral : 22.598 169.940 2808 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.84 % Allowed : 20.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1290 helix: 1.74 (0.22), residues: 637 sheet: 0.00 (0.45), residues: 133 loop : 0.47 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 958 HIS 0.004 0.001 HIS A 415 PHE 0.012 0.001 PHE A 323 TYR 0.023 0.001 TYR A 764 ARG 0.002 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 622) hydrogen bonds : angle 3.85554 ( 1682) covalent geometry : bond 0.00370 (13493) covalent geometry : angle 0.58773 (18733) *********************** 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 80 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 47 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.9524 (OUTLIER) cc_final: 0.9061 (t80) REVERT: A 260 GLN cc_start: 0.9354 (pt0) cc_final: 0.9037 (pt0) REVERT: A 671 GLU cc_start: 0.9600 (OUTLIER) cc_final: 0.9362 (mp0) REVERT: A 786 GLU cc_start: 0.8604 (mp0) cc_final: 0.8360 (mp0) REVERT: A 798 MET cc_start: 0.9299 (ttt) cc_final: 0.8890 (tmm) REVERT: A 806 MET cc_start: 0.8607 (ttt) cc_final: 0.8258 (tmm) REVERT: A 836 HIS cc_start: 0.8844 (m90) cc_final: 0.8561 (m90) REVERT: A 969 GLN cc_start: 0.9419 (tm-30) cc_final: 0.9170 (tm-30) REVERT: A 1014 GLN cc_start: 0.9576 (tt0) cc_final: 0.9236 (tt0) REVERT: A 1055 MET cc_start: 0.9087 (ppp) cc_final: 0.8043 (ppp) REVERT: A 1062 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9174 (tt) outliers start: 33 outliers final: 29 residues processed: 76 average time/residue: 0.2076 time to fit residues: 25.6175 Evaluate side-chains 77 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 45 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 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 310 LEU Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 420 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 15 optimal weight: 0.4980 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.057349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.034926 restraints weight = 61168.136| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 3.76 r_work: 0.2416 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13493 Z= 0.254 Angle : 0.635 10.882 18733 Z= 0.331 Chirality : 0.041 0.324 2085 Planarity : 0.004 0.047 1999 Dihedral : 22.647 170.506 2808 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.27 % Allowed : 20.57 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1290 helix: 1.83 (0.22), residues: 634 sheet: -0.16 (0.45), residues: 138 loop : 0.53 (0.30), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 958 HIS 0.005 0.001 HIS A1269 PHE 0.014 0.001 PHE A 323 TYR 0.022 0.001 TYR A 764 ARG 0.002 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 622) hydrogen bonds : angle 3.95867 ( 1682) covalent geometry : bond 0.00548 (13493) covalent geometry : angle 0.63509 (18733) *********************** 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 85 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 47 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 165 PHE cc_start: 0.9541 (OUTLIER) cc_final: 0.9088 (t80) REVERT: A 260 GLN cc_start: 0.9375 (pt0) cc_final: 0.9052 (pt0) REVERT: A 671 GLU cc_start: 0.9586 (OUTLIER) cc_final: 0.9329 (mp0) REVERT: A 786 GLU cc_start: 0.8616 (mp0) cc_final: 0.8339 (mp0) REVERT: A 798 MET cc_start: 0.9307 (ttt) cc_final: 0.8900 (tmm) REVERT: A 836 HIS cc_start: 0.8833 (m90) cc_final: 0.8566 (m-70) REVERT: A 969 GLN cc_start: 0.9447 (tm-30) cc_final: 0.9193 (tm-30) REVERT: A 1002 LYS cc_start: 0.9106 (mmtt) cc_final: 0.8742 (mttt) REVERT: A 1014 GLN cc_start: 0.9591 (tt0) cc_final: 0.9286 (tt0) REVERT: A 1055 MET cc_start: 0.9085 (ppp) cc_final: 0.7933 (ppp) REVERT: A 1062 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9166 (tt) outliers start: 38 outliers final: 34 residues processed: 81 average time/residue: 0.2015 time to fit residues: 26.6328 Evaluate side-chains 82 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 45 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 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 310 LEU Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 475 LEU 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 989 VAL 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 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 134 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 30.0000 chunk 105 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1143 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 = 0.3336 r_free = 0.3336 target = 0.058002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.035548 restraints weight = 60610.922| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 3.79 r_work: 0.2432 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2687 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= 0.189 Angle : 0.603 11.190 18733 Z= 0.313 Chirality : 0.040 0.327 2085 Planarity : 0.003 0.045 1999 Dihedral : 22.634 170.461 2808 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.10 % Allowed : 21.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1290 helix: 1.84 (0.21), residues: 635 sheet: -0.09 (0.45), residues: 138 loop : 0.57 (0.30), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 958 HIS 0.004 0.001 HIS A1269 PHE 0.013 0.001 PHE A 323 TYR 0.022 0.001 TYR A 764 ARG 0.002 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 622) hydrogen bonds : angle 3.87853 ( 1682) covalent geometry : bond 0.00412 (13493) covalent geometry : angle 0.60321 (18733) ********************** 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 83 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 47 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: A 165 PHE cc_start: 0.9553 (OUTLIER) cc_final: 0.9097 (t80) REVERT: A 260 GLN cc_start: 0.9381 (pt0) cc_final: 0.9056 (pt0) REVERT: A 671 GLU cc_start: 0.9591 (OUTLIER) cc_final: 0.9361 (mp0) REVERT: A 786 GLU cc_start: 0.8588 (mp0) cc_final: 0.8366 (mp0) REVERT: A 798 MET cc_start: 0.9314 (ttt) cc_final: 0.8925 (tmm) REVERT: A 806 MET cc_start: 0.8491 (ttt) cc_final: 0.8267 (tmm) REVERT: A 836 HIS cc_start: 0.8868 (m90) cc_final: 0.8602 (m-70) REVERT: A 1002 LYS cc_start: 0.9117 (mmtt) cc_final: 0.8753 (mttt) REVERT: A 1014 GLN cc_start: 0.9555 (tt0) cc_final: 0.9278 (tt0) REVERT: A 1055 MET cc_start: 0.9087 (ppp) cc_final: 0.8099 (ppp) REVERT: A 1062 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9195 (tt) outliers start: 36 outliers final: 32 residues processed: 78 average time/residue: 0.2151 time to fit residues: 28.3156 Evaluate side-chains 82 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 47 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 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 310 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 475 LEU 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 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 32 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 0.0470 chunk 111 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 0.2980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 HIS A1116 HIS A1143 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.059566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.037348 restraints weight = 60035.745| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 3.86 r_work: 0.2502 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2642 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= 0.117 Angle : 0.587 11.924 18733 Z= 0.301 Chirality : 0.039 0.306 2085 Planarity : 0.003 0.041 1999 Dihedral : 22.472 171.751 2808 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.18 % Allowed : 21.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1290 helix: 1.83 (0.21), residues: 636 sheet: 0.16 (0.45), residues: 133 loop : 0.54 (0.30), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 958 HIS 0.004 0.001 HIS A 415 PHE 0.011 0.001 PHE A 323 TYR 0.022 0.001 TYR A 764 ARG 0.002 0.000 ARG A1003 Details of bonding type rmsd hydrogen bonds : bond 0.03019 ( 622) hydrogen bonds : angle 3.73795 ( 1682) covalent geometry : bond 0.00258 (13493) covalent geometry : angle 0.58708 (18733) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6556.28 seconds wall clock time: 118 minutes 57.86 seconds (7137.86 seconds total)