Starting phenix.real_space_refine on Sat Aug 23 14:11:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfo_40446/08_2025/8sfo_40446.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfo_40446/08_2025/8sfo_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_2025/8sfo_40446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfo_40446/08_2025/8sfo_40446.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfo_40446/08_2025/8sfo_40446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfo_40446/08_2025/8sfo_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-2.0-5787/lib/python3.9/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: 2.47, per 1000 atoms: 0.20 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: 0.90 Conformation dependent library (CDL) restraints added in 320.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.30 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: 2.41 Time building geometry restraints manager: 1.18 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' DG D 24 " pdb=" O3' DG D 24 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.88e+00 bond pdb=" C3' DA D 32 " pdb=" O3' DA D 32 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.73e+00 bond pdb=" CB GLU A 350 " pdb=" CG GLU A 350 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" CB ASN A 354 " pdb=" CG ASN A 354 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.97e+00 bond pdb=" CA ILE A 905 " pdb=" C ILE A 905 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.27e-02 6.20e+03 1.86e+00 ... (remaining 13124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 18193 5.02 - 10.04: 50 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=" O3' DC C 7 " pdb=" P DA C 8 " pdb=" OP1 DA C 8 " ideal model delta sigma weight residual 108.00 125.09 -17.09 3.00e+00 1.11e-01 3.24e+01 angle pdb=" OP1 DA D 7 " pdb=" P DA D 7 " pdb=" OP2 DA D 7 " ideal model delta sigma weight residual 120.00 103.52 16.48 3.00e+00 1.11e-01 3.02e+01 angle pdb=" OP1 DA C 8 " pdb=" P DA C 8 " pdb=" OP2 DA C 8 " ideal model delta sigma weight residual 120.00 106.10 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CG1 ILE A 905 " pdb=" CB ILE A 905 " pdb=" CG2 ILE A 905 " ideal model delta sigma weight residual 110.70 97.09 13.61 3.00e+00 1.11e-01 2.06e+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 - 0.147: 2013 0.147 - 0.295: 7 0.295 - 0.442: 16 0.442 - 0.590: 0 0.590 - 0.737: 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 2.35 -3.08 -0.74 2.00e-01 2.50e+01 1.36e+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 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.26e+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 2.35 -2.77 -0.43 2.00e-01 2.50e+01 4.60e+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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.170 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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= 0.174 Angle : 0.863 25.108 18268 Z= 0.409 Chirality : 0.059 0.737 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 aren 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 covalent geometry : bond 0.00386 (13129) covalent geometry : angle 0.86271 (18268) hydrogen bonds : bond 0.14264 ( 594) hydrogen bonds : angle 6.13755 ( 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 : 0.283 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: 0.1104 time to fit residues: 9.3883 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 : 0.441 ------------------------------------------------------------------------------- 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: 5.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 116 ASN ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS A 630 ASN A 941 GLN A1024 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.044034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.030176 restraints weight = 71743.422| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 4.19 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13129 Z= 0.346 Angle : 0.690 10.550 18268 Z= 0.365 Chirality : 0.042 0.165 2038 Planarity : 0.004 0.041 1922 Dihedral : 21.314 172.615 2823 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.35 % Allowed : 12.82 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.25), residues: 1234 helix: 1.67 (0.21), residues: 617 sheet: -0.36 (0.45), residues: 119 loop : 0.35 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 176 TYR 0.017 0.002 TYR A 595 PHE 0.019 0.002 PHE A 198 TRP 0.009 0.002 TRP A1085 HIS 0.006 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00730 (13129) covalent geometry : angle 0.68997 (18268) hydrogen bonds : bond 0.04552 ( 594) hydrogen bonds : angle 4.31901 ( 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 50 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 HIS cc_start: 0.8514 (OUTLIER) cc_final: 0.8238 (p-80) REVERT: A 568 MET cc_start: 0.9201 (pmm) cc_final: 0.8904 (pmm) REVERT: A 604 MET cc_start: 0.9397 (mmm) cc_final: 0.9160 (mmm) REVERT: A 1225 MET cc_start: 0.9279 (mmt) cc_final: 0.8937 (mmm) outliers start: 15 outliers final: 7 residues processed: 49 average time/residue: 0.0872 time to fit residues: 6.7099 Evaluate side-chains 33 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU 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: 0.9980 chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.045472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.031564 restraints weight = 71370.098| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 4.11 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13129 Z= 0.122 Angle : 0.520 10.772 18268 Z= 0.279 Chirality : 0.038 0.255 2038 Planarity : 0.003 0.038 1922 Dihedral : 21.197 173.098 2823 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.08 % Allowed : 13.54 % 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 aren not related in a simple way. whole: 1.72 (0.25), residues: 1234 helix: 2.16 (0.22), residues: 613 sheet: -0.49 (0.44), residues: 129 loop : 0.41 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 574 TYR 0.017 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 A1280 Details of bonding type rmsd covalent geometry : bond 0.00263 (13129) covalent geometry : angle 0.51999 (18268) hydrogen bonds : bond 0.03234 ( 594) hydrogen bonds : angle 3.85973 ( 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 40 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8367 (mm110) REVERT: A 174 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8695 (mm-30) REVERT: A 176 ARG cc_start: 0.9677 (OUTLIER) cc_final: 0.8816 (tpp80) REVERT: A 415 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.8238 (p-80) REVERT: A 537 MET cc_start: 0.8964 (mtt) cc_final: 0.8750 (mmt) REVERT: A 568 MET cc_start: 0.9158 (pmm) cc_final: 0.8836 (pmm) REVERT: A 593 MET cc_start: 0.9095 (tmm) cc_final: 0.8802 (tmm) REVERT: A 604 MET cc_start: 0.9404 (mmm) cc_final: 0.9092 (mmm) REVERT: A 965 LYS cc_start: 0.8930 (tttt) cc_final: 0.8651 (tttp) outliers start: 12 outliers final: 5 residues processed: 40 average time/residue: 0.0967 time to fit residues: 6.0817 Evaluate side-chains 35 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 415 HIS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1299 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.044919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.031058 restraints weight = 71263.611| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 4.07 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13129 Z= 0.158 Angle : 0.513 10.912 18268 Z= 0.277 Chirality : 0.037 0.190 2038 Planarity : 0.003 0.039 1922 Dihedral : 21.150 175.564 2823 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.44 % Allowed : 14.17 % 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 aren not related in a simple way. whole: 1.95 (0.25), residues: 1234 helix: 2.37 (0.22), residues: 615 sheet: -0.47 (0.44), residues: 127 loop : 0.50 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.015 0.001 TYR A 595 PHE 0.010 0.001 PHE A1117 TRP 0.009 0.001 TRP A1085 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00342 (13129) covalent geometry : angle 0.51289 (18268) hydrogen bonds : bond 0.03164 ( 594) hydrogen bonds : angle 3.73395 ( 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 43 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 27 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8392 (mm110) REVERT: A 174 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8740 (mm-30) REVERT: A 176 ARG cc_start: 0.9677 (OUTLIER) cc_final: 0.8757 (tpp80) REVERT: A 415 HIS cc_start: 0.8577 (OUTLIER) cc_final: 0.8272 (p-80) REVERT: A 537 MET cc_start: 0.9025 (mtt) cc_final: 0.8682 (mmt) REVERT: A 568 MET cc_start: 0.9079 (pmm) cc_final: 0.8829 (pmm) REVERT: A 593 MET cc_start: 0.9100 (tmm) cc_final: 0.8773 (tmm) REVERT: A 965 LYS cc_start: 0.8953 (tttt) cc_final: 0.8718 (tptt) REVERT: A 1021 ASP cc_start: 0.9360 (m-30) cc_final: 0.9085 (m-30) outliers start: 16 outliers final: 6 residues processed: 43 average time/residue: 0.1013 time to fit residues: 6.7999 Evaluate side-chains 33 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 285 ILE Chi-restraints excluded: chain A residue 389 LEU 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 1278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 67 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 129 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.044952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.031101 restraints weight = 71150.536| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 4.10 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13129 Z= 0.138 Angle : 0.512 10.856 18268 Z= 0.273 Chirality : 0.038 0.265 2038 Planarity : 0.003 0.037 1922 Dihedral : 21.140 177.196 2823 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.17 % Allowed : 15.07 % 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 aren not related in a simple way. whole: 2.17 (0.25), residues: 1234 helix: 2.56 (0.22), residues: 610 sheet: -0.47 (0.43), residues: 129 loop : 0.65 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.015 0.001 TYR A 595 PHE 0.011 0.001 PHE A1117 TRP 0.009 0.001 TRP A1085 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00298 (13129) covalent geometry : angle 0.51187 (18268) hydrogen bonds : bond 0.02978 ( 594) hydrogen bonds : angle 3.62142 ( 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 38 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8381 (mm110) REVERT: A 174 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8821 (mm-30) REVERT: A 176 ARG cc_start: 0.9657 (OUTLIER) cc_final: 0.8791 (tpp80) REVERT: A 415 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.8367 (p-80) REVERT: A 537 MET cc_start: 0.9064 (mtt) cc_final: 0.8724 (mmt) REVERT: A 593 MET cc_start: 0.9093 (tmm) cc_final: 0.8771 (tmm) REVERT: A 965 LYS cc_start: 0.8938 (tttt) cc_final: 0.8698 (tptt) REVERT: A 1021 ASP cc_start: 0.9367 (m-30) cc_final: 0.9025 (m-30) outliers start: 13 outliers final: 8 residues processed: 38 average time/residue: 0.0880 time to fit residues: 5.3084 Evaluate side-chains 35 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 415 HIS 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 1278 LEU Chi-restraints excluded: chain A residue 1299 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 42 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 52 optimal weight: 0.0070 chunk 22 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 19 optimal weight: 0.0170 chunk 27 optimal weight: 6.9990 overall best weight: 1.3440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.045025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.031238 restraints weight = 70621.636| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 4.08 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13129 Z= 0.133 Angle : 0.499 11.557 18268 Z= 0.267 Chirality : 0.037 0.216 2038 Planarity : 0.003 0.036 1922 Dihedral : 21.057 179.474 2823 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.44 % Allowed : 14.89 % 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 aren not related in a simple way. whole: 2.30 (0.25), residues: 1234 helix: 2.65 (0.22), residues: 613 sheet: -0.20 (0.45), residues: 119 loop : 0.65 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1094 TYR 0.015 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 covalent geometry : bond 0.00288 (13129) covalent geometry : angle 0.49926 (18268) hydrogen bonds : bond 0.02883 ( 594) hydrogen bonds : angle 3.51678 ( 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 41 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 25 time to evaluate : 0.443 Fit side-chains REVERT: A 24 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8395 (mm110) REVERT: A 174 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8785 (mm-30) REVERT: A 176 ARG cc_start: 0.9667 (OUTLIER) cc_final: 0.8522 (tpp80) REVERT: A 415 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.8336 (p-80) REVERT: A 537 MET cc_start: 0.9089 (mtt) cc_final: 0.8755 (mmt) REVERT: A 593 MET cc_start: 0.9073 (tmm) cc_final: 0.8766 (tmm) REVERT: A 965 LYS cc_start: 0.8957 (tttt) cc_final: 0.8710 (tptt) REVERT: A 1021 ASP cc_start: 0.9389 (m-30) cc_final: 0.9030 (m-30) REVERT: A 1119 MET cc_start: 0.9033 (tpp) cc_final: 0.8748 (mmm) outliers start: 16 outliers final: 8 residues processed: 41 average time/residue: 0.0855 time to fit residues: 5.7851 Evaluate side-chains 34 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 251 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 415 HIS 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 1278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 127 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.044343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.030555 restraints weight = 70613.676| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 4.09 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13129 Z= 0.175 Angle : 0.527 12.251 18268 Z= 0.280 Chirality : 0.038 0.197 2038 Planarity : 0.003 0.037 1922 Dihedral : 21.024 179.648 2823 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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 aren not related in a simple way. whole: 2.35 (0.25), residues: 1234 helix: 2.75 (0.22), residues: 610 sheet: -0.17 (0.45), residues: 119 loop : 0.60 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1094 TYR 0.014 0.001 TYR A 595 PHE 0.011 0.001 PHE A 198 TRP 0.008 0.001 TRP A1085 HIS 0.007 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00375 (13129) covalent geometry : angle 0.52721 (18268) hydrogen bonds : bond 0.03151 ( 594) hydrogen bonds : angle 3.55910 ( 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 39 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 23 time to evaluate : 0.474 Fit side-chains REVERT: A 24 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8359 (mm110) REVERT: A 174 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8794 (mm-30) REVERT: A 176 ARG cc_start: 0.9663 (OUTLIER) cc_final: 0.8672 (tpp80) REVERT: A 415 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.8404 (p-80) REVERT: A 537 MET cc_start: 0.9129 (mtt) cc_final: 0.8771 (mmt) REVERT: A 593 MET cc_start: 0.9086 (tmm) cc_final: 0.8760 (tmm) REVERT: A 1021 ASP cc_start: 0.9410 (m-30) cc_final: 0.9044 (m-30) outliers start: 16 outliers final: 10 residues processed: 38 average time/residue: 0.1078 time to fit residues: 6.6923 Evaluate side-chains 36 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 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 415 HIS 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 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: 1.9990 chunk 133 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.044797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.031127 restraints weight = 69658.101| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 3.94 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13129 Z= 0.133 Angle : 0.508 13.133 18268 Z= 0.270 Chirality : 0.037 0.168 2038 Planarity : 0.003 0.038 1922 Dihedral : 20.974 179.117 2823 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.26 % Allowed : 15.16 % 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 aren not related in a simple way. whole: 2.38 (0.25), residues: 1234 helix: 2.76 (0.22), residues: 607 sheet: -0.13 (0.45), residues: 121 loop : 0.64 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 176 TYR 0.015 0.001 TYR A 595 PHE 0.010 0.001 PHE A1117 TRP 0.010 0.001 TRP A1085 HIS 0.006 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00289 (13129) covalent geometry : angle 0.50792 (18268) hydrogen bonds : bond 0.02912 ( 594) hydrogen bonds : angle 3.48849 ( 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 38 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.444 Fit side-chains REVERT: A 24 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8340 (mm110) REVERT: A 174 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8797 (mm-30) REVERT: A 176 ARG cc_start: 0.9655 (OUTLIER) cc_final: 0.8691 (tpp80) REVERT: A 415 HIS cc_start: 0.8682 (OUTLIER) cc_final: 0.8401 (p-80) REVERT: A 537 MET cc_start: 0.9094 (mtt) cc_final: 0.8788 (mmt) REVERT: A 593 MET cc_start: 0.9068 (tmm) cc_final: 0.8756 (tmm) REVERT: A 1021 ASP cc_start: 0.9414 (m-30) cc_final: 0.8986 (m-30) REVERT: A 1119 MET cc_start: 0.8960 (tpp) cc_final: 0.8658 (mmm) outliers start: 14 outliers final: 8 residues processed: 36 average time/residue: 0.1051 time to fit residues: 6.3364 Evaluate side-chains 33 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 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 415 HIS Chi-restraints excluded: chain A residue 873 VAL 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=1.50 ------------------------------------------------------------------------------- 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: 5.9990 chunk 37 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1290 GLN ** 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 = 0.3089 r_free = 0.3089 target = 0.042977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.029162 restraints weight = 73692.711| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 4.13 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 13129 Z= 0.327 Angle : 0.646 13.193 18268 Z= 0.340 Chirality : 0.041 0.175 2038 Planarity : 0.003 0.044 1922 Dihedral : 21.091 179.444 2823 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.17 % Allowed : 15.34 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.25), residues: 1234 helix: 2.54 (0.22), residues: 616 sheet: -0.46 (0.45), residues: 119 loop : 0.58 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 176 TYR 0.013 0.002 TYR A 83 PHE 0.017 0.001 PHE A 198 TRP 0.011 0.001 TRP A 382 HIS 0.010 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00694 (13129) covalent geometry : angle 0.64640 (18268) hydrogen bonds : bond 0.03997 ( 594) hydrogen bonds : angle 3.85115 ( 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 36 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8499 (mm110) REVERT: A 174 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8834 (mm-30) REVERT: A 415 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8574 (p-80) REVERT: A 537 MET cc_start: 0.9196 (mtt) cc_final: 0.8847 (mmt) REVERT: A 568 MET cc_start: 0.9513 (ptp) cc_final: 0.9038 (pmm) REVERT: A 905 ILE cc_start: 0.9380 (mt) cc_final: 0.9118 (mm) REVERT: A 1021 ASP cc_start: 0.9441 (m-30) cc_final: 0.9089 (m-30) outliers start: 13 outliers final: 10 residues processed: 35 average time/residue: 0.0985 time to fit residues: 5.7175 Evaluate side-chains 35 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 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 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: 10.0000 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.044385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.030600 restraints weight = 70912.818| |-----------------------------------------------------------------------------| r_work (start): 0.2623 rms_B_bonded: 4.10 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13129 Z= 0.126 Angle : 0.524 13.608 18268 Z= 0.276 Chirality : 0.037 0.244 2038 Planarity : 0.003 0.041 1922 Dihedral : 21.004 177.910 2823 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.17 % Allowed : 15.52 % 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 aren not related in a simple way. whole: 2.39 (0.25), residues: 1234 helix: 2.77 (0.22), residues: 608 sheet: -0.28 (0.45), residues: 121 loop : 0.68 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 574 TYR 0.016 0.001 TYR A 595 PHE 0.009 0.001 PHE A1117 TRP 0.011 0.001 TRP A1085 HIS 0.006 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00276 (13129) covalent geometry : angle 0.52392 (18268) hydrogen bonds : bond 0.02924 ( 594) hydrogen bonds : angle 3.53734 ( 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 36 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.452 Fit side-chains REVERT: A 24 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8294 (mm110) REVERT: A 174 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8826 (mm-30) REVERT: A 176 ARG cc_start: 0.9641 (OUTLIER) cc_final: 0.8721 (tpp80) REVERT: A 415 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8523 (p-80) REVERT: A 537 MET cc_start: 0.9116 (mtt) cc_final: 0.8837 (mmt) REVERT: A 568 MET cc_start: 0.9520 (ptp) cc_final: 0.9124 (pmm) REVERT: A 593 MET cc_start: 0.9094 (tmm) cc_final: 0.8787 (tmm) REVERT: A 905 ILE cc_start: 0.9352 (mt) cc_final: 0.9078 (mm) REVERT: A 1021 ASP cc_start: 0.9420 (m-30) cc_final: 0.9045 (m-30) REVERT: A 1119 MET cc_start: 0.8898 (tpp) cc_final: 0.8589 (mmm) outliers start: 13 outliers final: 8 residues processed: 35 average time/residue: 0.1033 time to fit residues: 6.0618 Evaluate side-chains 34 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 415 HIS Chi-restraints excluded: chain A residue 873 VAL 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: 0.7980 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.044451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.030664 restraints weight = 71504.686| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 4.05 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13129 Z= 0.134 Angle : 0.520 13.714 18268 Z= 0.275 Chirality : 0.037 0.177 2038 Planarity : 0.003 0.038 1922 Dihedral : 20.966 177.108 2823 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.08 % Allowed : 15.79 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.25), residues: 1234 helix: 2.77 (0.21), residues: 609 sheet: -0.22 (0.45), residues: 121 loop : 0.72 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 176 TYR 0.015 0.001 TYR A 595 PHE 0.009 0.001 PHE A1117 TRP 0.011 0.001 TRP A1085 HIS 0.006 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00290 (13129) covalent geometry : angle 0.52036 (18268) hydrogen bonds : bond 0.02912 ( 594) hydrogen bonds : angle 3.49450 ( 1619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.27 seconds wall clock time: 29 minutes 37.93 seconds (1777.93 seconds total)