Starting phenix.real_space_refine on Fri Jul 3 06:24:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfo_40446/07_2026/8sfo_40446.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfo_40446/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sfo_40446/07_2026/8sfo_40446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfo_40446/07_2026/8sfo_40446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sfo_40446/07_2026/8sfo_40446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfo_40446/07_2026/8sfo_40446.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-dev-6108/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: 2.91, per 1000 atoms: 0.23 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: 1.26 Conformation dependent library (CDL) restraints added in 448.3 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: 1.51 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: 3.34 Time building geometry restraints manager: 1.52 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: 18191 5.02 - 10.04: 52 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- 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= 0.329 Angle : 0.901 25.108 18268 Z= 0.566 Chirality : 0.061 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 0.00445 / 0.33 (13129) covalent geometry : angle 0.90053 / 0.57 (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 : 0.453 Fit side-chains 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: 0.1238 time to fit residues: 10.4994 Evaluate side-chains 35 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 10.0000 chunk 124 optimal weight: 10.0000 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 116 ASN A 630 ASN A 937 GLN A 941 GLN A1024 ASN A1227 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.045423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.031577 restraints weight = 70418.059| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 4.13 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 13129 Z= 0.345 Angle : 0.708 8.459 18268 Z= 0.389 Chirality : 0.044 0.269 2038 Planarity : 0.004 0.046 1922 Dihedral : 21.323 164.334 2823 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.26 % Allowed : 13.18 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.25), residues: 1234 helix: 1.58 (0.22), residues: 615 sheet: -0.68 (0.41), residues: 131 loop : 0.28 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1094 TYR 0.018 0.002 TYR A 595 PHE 0.014 0.001 PHE A 198 TRP 0.008 0.001 TRP A1085 HIS 0.009 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.35 (13129) covalent geometry : angle 0.70843 / 0.39 (18268) hydrogen bonds : bond 0.04742 / 3.07 ( 594) hydrogen bonds : angle 4.57391 / 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 48 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 604 MET cc_start: 0.9330 (mmm) cc_final: 0.9015 (mmm) outliers start: 14 outliers final: 7 residues processed: 47 average time/residue: 0.1049 time to fit residues: 7.9331 Evaluate side-chains 32 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 60 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 878 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.046407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.032611 restraints weight = 70460.899| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 4.18 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13129 Z= 0.127 Angle : 0.534 9.039 18268 Z= 0.304 Chirality : 0.041 0.306 2038 Planarity : 0.003 0.041 1922 Dihedral : 21.326 163.986 2823 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.08 % Allowed : 13.18 % Favored : 85.74 % 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: 1.50 (0.25), residues: 1234 helix: 1.95 (0.22), residues: 615 sheet: -0.60 (0.42), residues: 131 loop : 0.35 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 411 TYR 0.017 0.001 TYR A 595 PHE 0.015 0.001 PHE A 353 TRP 0.009 0.001 TRP A1085 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (13129) covalent geometry : angle 0.53438 / 0.30 (18268) hydrogen bonds : bond 0.03699 / 2.46 ( 594) hydrogen bonds : angle 4.11903 / 2.93 ( 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 42 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.9674 (OUTLIER) cc_final: 0.8845 (tpp80) REVERT: A 604 MET cc_start: 0.9342 (mmm) cc_final: 0.9036 (mmm) outliers start: 12 outliers final: 4 residues processed: 40 average time/residue: 0.1004 time to fit residues: 6.6348 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 : 0.412 ------------------------------------------------------------------------------- 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: 0.8980 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.045130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.031347 restraints weight = 71176.122| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 4.08 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13129 Z= 0.190 Angle : 0.551 7.908 18268 Z= 0.309 Chirality : 0.041 0.293 2038 Planarity : 0.003 0.038 1922 Dihedral : 21.307 166.174 2823 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.08 % Allowed : 14.08 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.25), residues: 1234 helix: 2.25 (0.22), residues: 616 sheet: -0.66 (0.43), residues: 119 loop : 0.39 (0.30), residues: 499 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 0.012 0.001 PHE A 198 TRP 0.009 0.001 TRP A1085 HIS 0.005 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (13129) covalent geometry : angle 0.55083 / 0.31 (18268) hydrogen bonds : bond 0.03753 / 2.47 ( 594) hydrogen bonds : angle 3.93354 / 2.80 ( 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 40 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8374 (mm110) REVERT: A 174 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8698 (mm-30) REVERT: A 176 ARG cc_start: 0.9673 (OUTLIER) cc_final: 0.8767 (tpp80) REVERT: A 604 MET cc_start: 0.9386 (mmm) cc_final: 0.9049 (mmm) outliers start: 12 outliers final: 8 residues processed: 40 average time/residue: 0.0980 time to fit residues: 6.4411 Evaluate side-chains 35 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 1199 ILE 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: 0.6980 chunk 80 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 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: 6.9990 chunk 50 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.044498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.030518 restraints weight = 71767.712| |-----------------------------------------------------------------------------| r_work (start): 0.2603 rms_B_bonded: 4.21 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2038 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= 0.211 Angle : 0.560 9.445 18268 Z= 0.312 Chirality : 0.041 0.294 2038 Planarity : 0.003 0.040 1922 Dihedral : 21.284 166.382 2823 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.53 % Allowed : 14.08 % Favored : 84.39 % 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: 1.90 (0.25), residues: 1234 helix: 2.38 (0.22), residues: 615 sheet: -0.64 (0.43), residues: 119 loop : 0.43 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.016 0.001 TYR A 595 PHE 0.012 0.001 PHE A 198 TRP 0.010 0.001 TRP A1085 HIS 0.005 0.001 HIS A 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 (13129) covalent geometry : angle 0.55961 / 0.31 (18268) hydrogen bonds : bond 0.03657 / 2.41 ( 594) hydrogen bonds : angle 3.91393 / 2.79 ( 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 45 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 28 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8364 (mm110) REVERT: A 174 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8711 (mm-30) REVERT: A 176 ARG cc_start: 0.9657 (OUTLIER) cc_final: 0.8764 (tpp80) REVERT: A 248 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8834 (mp-120) REVERT: A 310 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8814 (mm) REVERT: A 604 MET cc_start: 0.9395 (mmm) cc_final: 0.9100 (mmm) REVERT: A 784 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8864 (tt0) REVERT: A 1260 MET cc_start: 0.9216 (mmt) cc_final: 0.8931 (mmm) outliers start: 17 outliers final: 10 residues processed: 44 average time/residue: 0.1015 time to fit residues: 7.1550 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 : 0.295 ------------------------------------------------------------------------------- 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 784 GLN 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 1278 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 42 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.0050 chunk 90 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 134 optimal weight: 30.0000 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.045170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.031336 restraints weight = 70807.436| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 4.08 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13129 Z= 0.134 Angle : 0.521 12.327 18268 Z= 0.291 Chirality : 0.040 0.305 2038 Planarity : 0.003 0.036 1922 Dihedral : 21.245 166.677 2823 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.35 % Allowed : 14.44 % Favored : 84.21 % 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: 2.01 (0.25), residues: 1234 helix: 2.44 (0.22), residues: 615 sheet: -0.57 (0.44), residues: 119 loop : 0.51 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 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 0.00254 / 0.13 (13129) covalent geometry : angle 0.52073 / 0.29 (18268) hydrogen bonds : bond 0.03301 / 2.22 ( 594) hydrogen bonds : angle 3.77524 / 2.69 ( 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 42 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8321 (mm110) REVERT: A 174 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8738 (mm-30) REVERT: A 176 ARG cc_start: 0.9641 (OUTLIER) cc_final: 0.8814 (tpp80) REVERT: A 310 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8764 (mm) outliers start: 15 outliers final: 10 residues processed: 42 average time/residue: 0.0998 time to fit residues: 6.8102 Evaluate side-chains 39 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 176 ARG 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 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 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: 10.0000 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 = 0.3128 r_free = 0.3128 target = 0.044772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.030907 restraints weight = 70902.748| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 4.10 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13129 Z= 0.163 Angle : 0.529 12.735 18268 Z= 0.294 Chirality : 0.040 0.304 2038 Planarity : 0.003 0.035 1922 Dihedral : 21.216 167.767 2823 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.62 % Allowed : 14.44 % Favored : 83.94 % 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: 2.07 (0.25), residues: 1234 helix: 2.50 (0.22), residues: 615 sheet: -0.53 (0.44), residues: 119 loop : 0.52 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 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 0.00320 / 0.16 (13129) covalent geometry : angle 0.52865 / 0.29 (18268) hydrogen bonds : bond 0.03371 / 2.26 ( 594) hydrogen bonds : angle 3.75484 / 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 43 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8373 (mm110) REVERT: A 174 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8752 (mm-30) REVERT: A 176 ARG cc_start: 0.9643 (OUTLIER) cc_final: 0.8801 (tpp80) REVERT: A 310 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8785 (mm) REVERT: A 604 MET cc_start: 0.9352 (mmm) cc_final: 0.9092 (mmm) REVERT: A 786 GLU cc_start: 0.8013 (mp0) cc_final: 0.7532 (mp0) outliers start: 18 outliers final: 13 residues processed: 42 average time/residue: 0.0971 time to fit residues: 6.6786 Evaluate side-chains 41 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 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 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 1210 HIS 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: 0.7980 chunk 133 optimal weight: 40.0000 chunk 105 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 0.0270 chunk 134 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 0.0030 overall best weight: 0.5048 ------------------------------------------------------------------------------- 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 = 0.3155 r_free = 0.3155 target = 0.045738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.031682 restraints weight = 69883.870| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 4.13 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13129 Z= 0.108 Angle : 0.510 13.150 18268 Z= 0.283 Chirality : 0.040 0.321 2038 Planarity : 0.003 0.033 1922 Dihedral : 21.174 168.047 2823 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.08 % Allowed : 14.89 % 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: 2.10 (0.25), residues: 1234 helix: 2.49 (0.22), residues: 613 sheet: -0.57 (0.43), residues: 129 loop : 0.64 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 341 TYR 0.016 0.001 TYR A 595 PHE 0.010 0.001 PHE A1117 TRP 0.010 0.001 TRP A1085 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.11 (13129) covalent geometry : angle 0.51012 / 0.28 (18268) hydrogen bonds : bond 0.03048 / 2.06 ( 594) hydrogen bonds : angle 3.64302 / 2.60 ( 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 42 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8331 (mm110) REVERT: A 174 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8808 (mm-30) REVERT: A 593 MET cc_start: 0.9088 (tmm) cc_final: 0.8770 (tmm) REVERT: A 786 GLU cc_start: 0.7906 (mp0) cc_final: 0.7452 (mp0) REVERT: A 1021 ASP cc_start: 0.9296 (m-30) cc_final: 0.9069 (m-30) outliers start: 12 outliers final: 8 residues processed: 42 average time/residue: 0.0926 time to fit residues: 6.7030 Evaluate side-chains 36 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 389 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1199 ILE 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: 6.9990 chunk 33 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 134 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 133 optimal weight: 40.0000 chunk 71 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.043837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.030019 restraints weight = 72067.805| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 4.11 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13129 Z= 0.292 Angle : 0.620 13.690 18268 Z= 0.334 Chirality : 0.042 0.293 2038 Planarity : 0.003 0.041 1922 Dihedral : 21.222 169.002 2823 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.26 % Allowed : 15.07 % 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: 2.15 (0.25), residues: 1234 helix: 2.60 (0.22), residues: 611 sheet: -0.55 (0.44), residues: 119 loop : 0.57 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.015 0.002 TYR A 595 PHE 0.015 0.001 PHE A 198 TRP 0.008 0.001 TRP A 382 HIS 0.008 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.29 (13129) covalent geometry : angle 0.61988 / 0.33 (18268) hydrogen bonds : bond 0.03960 / 2.61 ( 594) hydrogen bonds : angle 3.86616 / 2.76 ( 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 40 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8348 (mm110) REVERT: A 174 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8763 (mm-30) REVERT: A 310 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8766 (mm) REVERT: A 604 MET cc_start: 0.9301 (mmm) cc_final: 0.9025 (mmm) REVERT: A 786 GLU cc_start: 0.7969 (mp0) cc_final: 0.7564 (mp0) outliers start: 14 outliers final: 11 residues processed: 38 average time/residue: 0.0949 time to fit residues: 6.1709 Evaluate side-chains 38 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 1024 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 127 optimal weight: 40.0000 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 133 optimal weight: 40.0000 chunk 78 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.044165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.030350 restraints weight = 71075.538| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 4.05 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13129 Z= 0.195 Angle : 0.560 13.979 18268 Z= 0.306 Chirality : 0.041 0.304 2038 Planarity : 0.003 0.041 1922 Dihedral : 21.243 168.195 2823 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.17 % Allowed : 15.25 % Favored : 83.57 % 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: 2.20 (0.25), residues: 1234 helix: 2.61 (0.22), residues: 613 sheet: -0.53 (0.45), residues: 119 loop : 0.60 (0.30), residues: 502 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 0.006 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.20 (13129) covalent geometry : angle 0.55971 / 0.31 (18268) hydrogen bonds : bond 0.03498 / 2.34 ( 594) hydrogen bonds : angle 3.75447 / 2.68 ( 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 40 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.428 Fit side-chains REVERT: A 24 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8328 (mm110) REVERT: A 174 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8763 (mm-30) REVERT: A 310 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8767 (mm) REVERT: A 604 MET cc_start: 0.9300 (mmm) cc_final: 0.9037 (mmm) REVERT: A 786 GLU cc_start: 0.7929 (mp0) cc_final: 0.7564 (mp0) REVERT: A 1021 ASP cc_start: 0.9359 (m-30) cc_final: 0.9104 (m-30) outliers start: 13 outliers final: 11 residues processed: 39 average time/residue: 0.0817 time to fit residues: 5.7145 Evaluate side-chains 39 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 1024 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 113 optimal weight: 0.0670 chunk 126 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.1922 ------------------------------------------------------------------------------- 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 = 0.3138 r_free = 0.3138 target = 0.044871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.030999 restraints weight = 71059.924| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 4.02 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13129 Z= 0.126 Angle : 0.518 14.143 18268 Z= 0.287 Chirality : 0.040 0.317 2038 Planarity : 0.003 0.039 1922 Dihedral : 21.204 168.603 2823 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.17 % Allowed : 15.25 % Favored : 83.57 % 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: 2.29 (0.25), residues: 1234 helix: 2.65 (0.22), residues: 612 sheet: -0.38 (0.45), residues: 119 loop : 0.68 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 0.00238 / 0.13 (13129) covalent geometry : angle 0.51836 / 0.29 (18268) hydrogen bonds : bond 0.03187 / 2.16 ( 594) hydrogen bonds : angle 3.63474 / 2.59 ( 1619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1671.60 seconds wall clock time: 29 minutes 56.17 seconds (1796.17 seconds total)