Starting phenix.real_space_refine on Thu Aug 6 00:39:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfo_40446/08_2026/8sfo_40446.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfo_40446/08_2026/8sfo_40446.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/8sfo_40446/08_2026/8sfo_40446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfo_40446/08_2026/8sfo_40446.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfo_40446/08_2026/8sfo_40446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfo_40446/08_2026/8sfo_40446.cif" } 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= -0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 118 5.49 5 Mg 2 5.21 5 S 23 5.16 5 C 7660 2.51 5 N 2157 2.21 5 O 2646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12606 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 10138 Classifications: {'peptide': 1240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1193} Chain breaks: 2 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 826 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 6, 'rna3p': 32} 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} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.02, per 1000 atoms: 0.16 Number of scatterers: 12606 At special positions: 0 Unit cell: (90.24, 104.34, 142.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 23 16.00 P 118 15.00 Mg 2 11.99 O 2646 8.00 N 2157 7.00 C 7660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 435.4 milliseconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 9 sheets defined 55.8% alpha, 9.7% beta 40 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.734A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.572A pdb=" N HIS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN A 34 " --> pdb=" O HIS A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 67 Proline residue: A 52 - end of helix removed outlier: 4.063A pdb=" N ILE A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 88 through 112 removed outlier: 3.988A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.961A pdb=" N GLY A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.686A pdb=" N LEU A 137 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.768A pdb=" N LEU A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) 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 removed outlier: 3.663A pdb=" N ASN A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 196 through 215 removed outlier: 3.943A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 230 removed outlier: 4.043A pdb=" N GLU A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.696A pdb=" N PHE A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.939A pdb=" N SER A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.986A pdb=" N THR A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 359 removed outlier: 3.873A pdb=" N ILE A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 359' Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.540A pdb=" N HIS A 363 " --> pdb=" O ASP A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.765A pdb=" N HIS A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 428 through 452 removed outlier: 3.600A pdb=" N SER A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.578A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 522 removed outlier: 3.505A pdb=" N ASN A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 600 through 610 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 619 Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.574A pdb=" N ASN A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.693A 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 694 through 698 removed outlier: 4.295A pdb=" N SER A 697 " --> pdb=" O ASP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.909A pdb=" N TYR A 704 " --> pdb=" O SER A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 716 through 719 removed outlier: 3.786A pdb=" N TYR A 719 " --> pdb=" O PRO A 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 716 through 719' Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.519A pdb=" N PHE A 750 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.596A 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 861 through 866 removed outlier: 3.643A pdb=" N PHE A 864 " --> pdb=" O ASP A 861 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A 866 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 899 removed outlier: 3.912A pdb=" N ARG A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 892 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 955 Processing helix chain 'A' and resid 964 through 987 removed outlier: 3.558A pdb=" N GLN A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1007 Processing helix chain 'A' and resid 1015 through 1025 removed outlier: 3.933A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.763A pdb=" N THR A1087 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 3.916A 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 Processing helix chain 'A' and resid 1199 through 1205 removed outlier: 3.508A pdb=" N GLU A1205 " --> pdb=" O PRO A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.809A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1254 Processing helix chain 'A' and resid 1261 through 1282 removed outlier: 3.633A pdb=" N LEU A1277 " --> pdb=" O LYS A1273 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.815A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.116A 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 533 removed outlier: 4.815A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366 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 907 through 909 removed outlier: 7.278A pdb=" N ILE A 915 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER A 931 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 990 through 994 Processing sheet with id=AA7, first strand: chain 'A' and resid 1104 through 1106 Processing sheet with id=AA8, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA9, first strand: chain 'A' and resid 1159 through 1162 504 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 1.15 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: 2362 1.33 - 1.45: 3783 1.45 - 1.57: 6712 1.57 - 1.69: 234 1.69 - 1.81: 38 Bond restraints: 13129 Sorted by residual: bond pdb=" C3' DT D 35 " pdb=" C2' DT D 35 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.37e+01 bond pdb=" C3' DG D 24 " pdb=" O3' DG D 24 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.26e+01 bond pdb=" C3' DT D 2 " pdb=" C2' DT D 2 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DT D 28 " pdb=" C2' DT D 28 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DA C 39 " pdb=" C2' DA C 39 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.13e+00 ... (remaining 13124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 18190 5.02 - 10.04: 53 10.04 - 15.06: 22 15.06 - 20.09: 2 20.09 - 25.11: 1 Bond angle restraints: 18268 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 108.00 133.11 -25.11 3.00e+00 1.11e-01 7.00e+01 angle pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sigma weight residual 117.70 126.71 -9.01 1.20e+00 6.94e-01 5.64e+01 angle pdb=" N1 U B 12 " pdb=" C2 U B 12 " pdb=" O2 U B 12 " ideal model delta sigma weight residual 122.80 127.55 -4.75 7.00e-01 2.04e+00 4.61e+01 angle pdb=" O2 U B 12 " pdb=" C2 U B 12 " pdb=" N3 U B 12 " ideal model delta sigma weight residual 122.20 117.90 4.30 7.00e-01 2.04e+00 3.77e+01 angle pdb=" O4' DA C 8 " pdb=" C4' DA C 8 " pdb=" C3' DA C 8 " ideal model delta sigma weight residual 106.00 102.36 3.64 6.00e-01 2.78e+00 3.68e+01 ... (remaining 18263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 7080 31.27 - 62.54: 609 62.54 - 93.81: 46 93.81 - 125.09: 3 125.09 - 156.36: 3 Dihedral angle restraints: 7741 sinusoidal: 4083 harmonic: 3658 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 49.49 150.51 1 1.50e+01 4.44e-03 7.98e+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 76.88 123.12 1 1.50e+01 4.44e-03 6.60e+01 dihedral pdb=" CA PHE A 598 " pdb=" C PHE A 598 " pdb=" N PRO A 599 " pdb=" CA PRO A 599 " ideal model delta harmonic sigma weight residual -180.00 -149.41 -30.59 0 5.00e+00 4.00e-02 3.74e+01 ... (remaining 7738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2011 0.149 - 0.299: 9 0.299 - 0.448: 16 0.448 - 0.598: 0 0.598 - 0.747: 2 Chirality restraints: 2038 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 2.34 -3.08 -0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" P DA C 8 " pdb=" OP1 DA C 8 " pdb=" OP2 DA C 8 " pdb=" O5' DA C 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" P DA C 28 " pdb=" OP1 DA C 28 " pdb=" OP2 DA C 28 " pdb=" O5' DA C 28 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.44 2.00e-01 2.50e+01 4.82e+00 ... (remaining 2035 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 146 " -0.038 2.00e-02 2.50e+03 7.42e-02 5.50e+01 pdb=" C LEU A 146 " 0.128 2.00e-02 2.50e+03 pdb=" O LEU A 146 " -0.048 2.00e-02 2.50e+03 pdb=" N GLY A 147 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC C 12 " -0.018 2.00e-02 2.50e+03 2.36e-02 1.25e+01 pdb=" N1 DC C 12 " 0.056 2.00e-02 2.50e+03 pdb=" C2 DC C 12 " -0.037 2.00e-02 2.50e+03 pdb=" O2 DC C 12 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC C 12 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DC C 12 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC C 12 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DC C 12 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC C 12 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 103 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C ARG A 103 " -0.046 2.00e-02 2.50e+03 pdb=" O ARG A 103 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 104 " 0.015 2.00e-02 2.50e+03 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 132 2.63 - 3.19: 10173 3.19 - 3.76: 20724 3.76 - 4.33: 27593 4.33 - 4.90: 44032 Nonbonded interactions: 102654 Sorted by model distance: nonbonded pdb=" OP1 DC D 31 " pdb="MG MG A1402 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP A 908 " pdb="MG MG A1401 " model vdw 2.141 2.170 nonbonded pdb=" O ASN A1090 " pdb=" OG SER A1093 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 109 " pdb=" OD1 ASN A 116 " model vdw 2.281 3.040 nonbonded pdb=" O LYS A1158 " pdb=" OH TYR A1236 " model vdw 2.287 3.040 ... (remaining 102649 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.500 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 : 0.004 0.064 13129 Z= 0.331 Angle : 0.921 25.108 18268 Z= 0.587 Chirality : 0.064 0.747 2038 Planarity : 0.005 0.074 1922 Dihedral : 20.068 156.358 5373 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.18 % Allowed : 13.63 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.22), residues: 1234 helix: -0.09 (0.19), residues: 603 sheet: -0.51 (0.43), residues: 131 loop : -0.19 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 574 TYR 0.021 0.002 TYR A 595 PHE 0.012 0.001 PHE A1103 TRP 0.008 0.001 TRP A 676 HIS 0.005 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.33 (13129) covalent geometry : angle 0.92099 / 0.59 (18268) hydrogen bonds : bond 0.14264 / 9.04 ( 594) hydrogen bonds : angle 6.13755 / 4.33 ( 1619) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 LEU cc_start: 0.8628 (tp) cc_final: 0.8396 (tp) outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 0.0917 time to fit residues: 7.7100 Evaluate side-chains 36 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 HIS A 630 ASN A 937 GLN A 941 GLN A1024 ASN A1227 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.045141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.031163 restraints weight = 70694.727| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 4.18 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 13129 Z= 0.355 Angle : 0.732 8.687 18268 Z= 0.398 Chirality : 0.045 0.319 2038 Planarity : 0.004 0.047 1922 Dihedral : 21.279 168.172 2823 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.17 % Allowed : 13.45 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1234 helix: 1.62 (0.22), residues: 616 sheet: -0.70 (0.41), residues: 131 loop : 0.28 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 386 TYR 0.019 0.002 TYR A 595 PHE 0.015 0.002 PHE A 198 TRP 0.009 0.001 TRP A1085 HIS 0.010 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.35 (13129) covalent geometry : angle 0.73227 / 0.40 (18268) hydrogen bonds : bond 0.04671 / 3.02 ( 594) hydrogen bonds : angle 4.57518 / 3.26 ( 1619) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 415 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.8145 (p90) REVERT: A 604 MET cc_start: 0.9346 (mmm) cc_final: 0.9017 (mmm) REVERT: A 965 LYS cc_start: 0.9166 (ttpp) cc_final: 0.8799 (tttp) outliers start: 13 outliers final: 6 residues processed: 46 average time/residue: 0.0809 time to fit residues: 6.0809 Evaluate side-chains 33 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 HIS A 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.046241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.032460 restraints weight = 70369.997| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 4.18 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13129 Z= 0.133 Angle : 0.536 8.624 18268 Z= 0.304 Chirality : 0.041 0.339 2038 Planarity : 0.003 0.042 1922 Dihedral : 21.275 166.131 2823 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.08 % Allowed : 13.27 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.25), residues: 1234 helix: 1.95 (0.22), residues: 618 sheet: -0.62 (0.42), residues: 131 loop : 0.38 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.018 0.001 TYR A 595 PHE 0.014 0.001 PHE A 353 TRP 0.009 0.001 TRP A1085 HIS 0.003 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (13129) covalent geometry : angle 0.53646 / 0.30 (18268) hydrogen bonds : bond 0.03679 / 2.44 ( 594) hydrogen bonds : angle 4.08817 / 2.91 ( 1619) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.9673 (OUTLIER) cc_final: 0.8837 (tpp80) REVERT: A 604 MET cc_start: 0.9345 (mmm) cc_final: 0.9039 (mmm) REVERT: A 965 LYS cc_start: 0.9116 (ttpp) cc_final: 0.8784 (tttt) REVERT: A 1119 MET cc_start: 0.9370 (tpp) cc_final: 0.9165 (tpp) outliers start: 12 outliers final: 4 residues processed: 40 average time/residue: 0.0951 time to fit residues: 6.1830 Evaluate side-chains 31 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 134 optimal weight: 30.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.045462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.031680 restraints weight = 71016.514| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 4.11 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13129 Z= 0.183 Angle : 0.553 9.292 18268 Z= 0.308 Chirality : 0.041 0.328 2038 Planarity : 0.003 0.038 1922 Dihedral : 21.268 168.078 2823 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.99 % Allowed : 13.63 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.25), residues: 1234 helix: 2.24 (0.22), residues: 619 sheet: -0.65 (0.43), residues: 119 loop : 0.37 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 411 TYR 0.015 0.001 TYR A 595 PHE 0.011 0.001 PHE A 198 TRP 0.009 0.001 TRP A1085 HIS 0.007 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (13129) covalent geometry : angle 0.55264 / 0.31 (18268) hydrogen bonds : bond 0.03664 / 2.41 ( 594) hydrogen bonds : angle 3.94138 / 2.81 ( 1619) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8323 (mm110) REVERT: A 174 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8702 (mm-30) REVERT: A 176 ARG cc_start: 0.9677 (OUTLIER) cc_final: 0.8770 (tpp80) REVERT: A 568 MET cc_start: 0.9121 (pmm) cc_final: 0.8850 (pmm) REVERT: A 604 MET cc_start: 0.9368 (mmm) cc_final: 0.9027 (mmm) REVERT: A 965 LYS cc_start: 0.9131 (ttpp) cc_final: 0.8773 (tttp) outliers start: 11 outliers final: 7 residues processed: 42 average time/residue: 0.0968 time to fit residues: 6.4724 Evaluate side-chains 35 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN A1024 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.043867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.030034 restraints weight = 72752.839| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 4.03 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13129 Z= 0.290 Angle : 0.653 11.130 18268 Z= 0.351 Chirality : 0.043 0.312 2038 Planarity : 0.003 0.040 1922 Dihedral : 21.290 168.366 2823 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.62 % Allowed : 13.81 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.25), residues: 1234 helix: 2.23 (0.22), residues: 616 sheet: -0.72 (0.43), residues: 119 loop : 0.42 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 176 TYR 0.015 0.002 TYR A 595 PHE 0.016 0.002 PHE A 198 TRP 0.010 0.001 TRP A1085 HIS 0.007 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.29 (13129) covalent geometry : angle 0.65333 / 0.35 (18268) hydrogen bonds : bond 0.04196 / 2.73 ( 594) hydrogen bonds : angle 4.08647 / 2.91 ( 1619) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 28 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8343 (mm110) REVERT: A 174 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8695 (mm-30) REVERT: A 248 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8892 (mp-120) REVERT: A 310 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8816 (mm) REVERT: A 604 MET cc_start: 0.9402 (mmm) cc_final: 0.9111 (mmm) REVERT: A 786 GLU cc_start: 0.8169 (mp0) cc_final: 0.7932 (mp0) REVERT: A 965 LYS cc_start: 0.9190 (ttpp) cc_final: 0.8890 (tttt) outliers start: 18 outliers final: 12 residues processed: 44 average time/residue: 0.0894 time to fit residues: 6.2229 Evaluate side-chains 40 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1216 VAL Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 42 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 134 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.044711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.030726 restraints weight = 70649.573| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 4.17 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13129 Z= 0.138 Angle : 0.529 12.345 18268 Z= 0.295 Chirality : 0.041 0.334 2038 Planarity : 0.003 0.038 1922 Dihedral : 21.241 168.179 2823 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.44 % Allowed : 14.53 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.25), residues: 1234 helix: 2.41 (0.22), residues: 616 sheet: -0.55 (0.44), residues: 119 loop : 0.48 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.017 0.001 TYR A 595 PHE 0.011 0.001 PHE A1117 TRP 0.011 0.001 TRP A1085 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (13129) covalent geometry : angle 0.52945 / 0.30 (18268) hydrogen bonds : bond 0.03427 / 2.30 ( 594) hydrogen bonds : angle 3.84156 / 2.74 ( 1619) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 28 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8364 (mm110) REVERT: A 174 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8680 (mm-30) REVERT: A 176 ARG cc_start: 0.9647 (OUTLIER) cc_final: 0.8802 (tpp80) REVERT: A 965 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8740 (tttp) outliers start: 16 outliers final: 13 residues processed: 43 average time/residue: 0.0964 time to fit residues: 6.4654 Evaluate side-chains 40 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 127 optimal weight: 40.0000 chunk 3 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1024 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.045111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.031136 restraints weight = 70509.526| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 4.10 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13129 Z= 0.119 Angle : 0.518 12.650 18268 Z= 0.288 Chirality : 0.040 0.341 2038 Planarity : 0.003 0.035 1922 Dihedral : 21.189 169.024 2823 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.44 % Allowed : 14.80 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.25), residues: 1234 helix: 2.42 (0.22), residues: 617 sheet: -0.64 (0.43), residues: 129 loop : 0.57 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 176 TYR 0.016 0.001 TYR A 595 PHE 0.010 0.001 PHE A1117 TRP 0.010 0.001 TRP A1085 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.12 (13129) covalent geometry : angle 0.51805 / 0.29 (18268) hydrogen bonds : bond 0.03279 / 2.21 ( 594) hydrogen bonds : angle 3.75572 / 2.68 ( 1619) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 28 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8372 (mm110) REVERT: A 174 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8724 (mm-30) REVERT: A 310 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8756 (mm) REVERT: A 965 LYS cc_start: 0.9095 (ttpp) cc_final: 0.8717 (tttp) outliers start: 16 outliers final: 10 residues processed: 43 average time/residue: 0.0840 time to fit residues: 5.8007 Evaluate side-chains 36 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 24 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 62 optimal weight: 0.2980 chunk 133 optimal weight: 40.0000 chunk 105 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 134 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.044806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.030926 restraints weight = 70141.270| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 4.04 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13129 Z= 0.155 Angle : 0.536 12.126 18268 Z= 0.295 Chirality : 0.041 0.339 2038 Planarity : 0.003 0.036 1922 Dihedral : 21.159 170.051 2823 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.35 % Allowed : 14.98 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.25), residues: 1234 helix: 2.47 (0.22), residues: 619 sheet: -0.62 (0.43), residues: 129 loop : 0.59 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.016 0.001 TYR A 595 PHE 0.011 0.001 PHE A1117 TRP 0.010 0.001 TRP A1085 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (13129) covalent geometry : angle 0.53589 / 0.29 (18268) hydrogen bonds : bond 0.03345 / 2.24 ( 594) hydrogen bonds : angle 3.74726 / 2.67 ( 1619) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8380 (mm110) REVERT: A 174 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8732 (mm-30) REVERT: A 176 ARG cc_start: 0.9643 (OUTLIER) cc_final: 0.8806 (tpp80) REVERT: A 310 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8797 (mm) REVERT: A 965 LYS cc_start: 0.9104 (ttpp) cc_final: 0.8816 (tttt) outliers start: 15 outliers final: 12 residues processed: 39 average time/residue: 0.0909 time to fit residues: 5.6265 Evaluate side-chains 40 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 78 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 134 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 133 optimal weight: 40.0000 chunk 71 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 HIS A 890 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.043696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.029814 restraints weight = 71244.420| |-----------------------------------------------------------------------------| r_work (start): 0.2597 rms_B_bonded: 4.02 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13129 Z= 0.231 Angle : 0.600 14.466 18268 Z= 0.322 Chirality : 0.042 0.328 2038 Planarity : 0.003 0.038 1922 Dihedral : 21.208 170.161 2823 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.62 % Allowed : 14.98 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.25), residues: 1234 helix: 2.59 (0.22), residues: 612 sheet: -0.60 (0.45), residues: 119 loop : 0.53 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.015 0.001 TYR A 595 PHE 0.014 0.001 PHE A 198 TRP 0.009 0.001 TRP A1085 HIS 0.008 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.23 (13129) covalent geometry : angle 0.60000 / 0.32 (18268) hydrogen bonds : bond 0.03838 / 2.54 ( 594) hydrogen bonds : angle 3.85923 / 2.75 ( 1619) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.396 Fit side-chains REVERT: A 24 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8374 (mm110) REVERT: A 174 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8749 (mm-30) REVERT: A 176 ARG cc_start: 0.9655 (OUTLIER) cc_final: 0.8747 (tpp80) REVERT: A 604 MET cc_start: 0.9306 (mmm) cc_final: 0.9055 (mmm) REVERT: A 965 LYS cc_start: 0.9145 (ttpp) cc_final: 0.8811 (tttt) outliers start: 18 outliers final: 13 residues processed: 42 average time/residue: 0.0860 time to fit residues: 5.9981 Evaluate side-chains 40 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1199 ILE Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 127 optimal weight: 40.0000 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 133 optimal weight: 40.0000 chunk 78 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.043711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.029856 restraints weight = 71475.329| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 4.06 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13129 Z= 0.233 Angle : 0.596 13.691 18268 Z= 0.322 Chirality : 0.042 0.332 2038 Planarity : 0.003 0.044 1922 Dihedral : 21.242 169.297 2823 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.35 % Allowed : 15.34 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.25), residues: 1234 helix: 2.49 (0.22), residues: 611 sheet: -0.70 (0.44), residues: 119 loop : 0.52 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 393 TYR 0.017 0.001 TYR A 595 PHE 0.014 0.001 PHE A1117 TRP 0.010 0.001 TRP A1085 HIS 0.008 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.23 (13129) covalent geometry : angle 0.59619 / 0.32 (18268) hydrogen bonds : bond 0.03746 / 2.50 ( 594) hydrogen bonds : angle 3.89297 / 2.76 ( 1619) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.399 Fit side-chains REVERT: A 24 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8498 (mm110) REVERT: A 174 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8746 (mm-30) REVERT: A 176 ARG cc_start: 0.9663 (OUTLIER) cc_final: 0.8504 (tpp80) REVERT: A 965 LYS cc_start: 0.9140 (ttpp) cc_final: 0.8723 (tttp) outliers start: 15 outliers final: 10 residues processed: 39 average time/residue: 0.0860 time to fit residues: 5.5224 Evaluate side-chains 38 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 1055 MET Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.044508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.030652 restraints weight = 70432.229| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 4.08 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13129 Z= 0.123 Angle : 0.544 14.576 18268 Z= 0.297 Chirality : 0.041 0.347 2038 Planarity : 0.003 0.038 1922 Dihedral : 21.190 169.904 2823 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.08 % Allowed : 15.70 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.25), residues: 1234 helix: 2.57 (0.22), residues: 610 sheet: -0.47 (0.45), residues: 119 loop : 0.63 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 103 TYR 0.019 0.001 TYR A 595 PHE 0.012 0.001 PHE A1117 TRP 0.013 0.001 TRP A1085 HIS 0.006 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (13129) covalent geometry : angle 0.54426 / 0.30 (18268) hydrogen bonds : bond 0.03278 / 2.23 ( 594) hydrogen bonds : angle 3.72937 / 2.64 ( 1619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1570.67 seconds wall clock time: 27 minutes 58.95 seconds (1678.95 seconds total)