Starting phenix.real_space_refine on Wed Mar 4 07:52:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nmd_0447/03_2026/6nmd_0447.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nmd_0447/03_2026/6nmd_0447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nmd_0447/03_2026/6nmd_0447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nmd_0447/03_2026/6nmd_0447.map" model { file = "/net/cci-nas-00/data/ceres_data/6nmd_0447/03_2026/6nmd_0447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nmd_0447/03_2026/6nmd_0447.cif" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 25 5.49 5 Mg 2 5.21 5 S 35 5.16 5 C 7451 2.51 5 N 1934 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11779 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1202, 9931 Classifications: {'peptide': 1202} Link IDs: {'PTRANS': 26, 'TRANS': 1175} Chain breaks: 3 Chain: "G" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 535 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna2p': 8, 'rna3p': 16} Chain: "B" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1305 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 3.00, per 1000 atoms: 0.25 Number of scatterers: 11779 At special positions: 0 Unit cell: (130.68, 109.08, 105.84, 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 35 16.00 P 25 15.00 Mg 2 11.99 O 2332 8.00 N 1934 7.00 C 7451 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: 1.06 Conformation dependent library (CDL) restraints added in 602.7 milliseconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 13 sheets defined 51.9% alpha, 4.9% beta 1 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 37 through 66 removed outlier: 5.043A pdb=" N TYR A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 73 through 83 removed outlier: 4.073A pdb=" N LEU A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 111 removed outlier: 3.737A pdb=" N GLU A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 removed outlier: 4.474A pdb=" N PHE A 119 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.881A pdb=" N ILE A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 124 " --> pdb=" O LYS A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 124' Processing helix chain 'A' and resid 136 through 142 removed outlier: 4.147A pdb=" N LEU A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 148 through 154 removed outlier: 4.162A pdb=" N GLY A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.846A pdb=" N ARG A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.927A pdb=" N SER A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 4.169A pdb=" N ASP A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA A 195 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 197 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.855A pdb=" N PHE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.719A pdb=" N LYS A 265 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.143A pdb=" N ILE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 Processing helix chain 'A' and resid 396 through 404 Processing helix chain 'A' and resid 409 through 433 removed outlier: 4.363A pdb=" N LYS A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.623A pdb=" N ASP A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 removed outlier: 3.702A pdb=" N ALA A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 560 through 563 removed outlier: 4.068A pdb=" N ALA A 563 " --> pdb=" O LYS A 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 628 through 646 removed outlier: 4.445A pdb=" N LYS A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 635 " --> pdb=" O ASP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 652 removed outlier: 3.940A pdb=" N ASN A 651 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 663 removed outlier: 3.882A pdb=" N TYR A 663 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 718 through 727 Processing helix chain 'A' and resid 786 through 790 removed outlier: 3.799A pdb=" N PHE A 789 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 4.058A pdb=" N ARG A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 822 " --> pdb=" O VAL A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 886 removed outlier: 3.710A pdb=" N GLU A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 4.443A pdb=" N VAL A 908 " --> pdb=" O ILE A 904 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N HIS A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 952 Processing helix chain 'A' and resid 953 through 956 Processing helix chain 'A' and resid 1020 through 1030 removed outlier: 4.398A pdb=" N LYS A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1120 through 1136 removed outlier: 4.182A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1129 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A1130 " --> pdb=" O SER A1126 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A1133 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1169 removed outlier: 4.165A pdb=" N ALA A1169 " --> pdb=" O ARG A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1199 removed outlier: 3.774A pdb=" N ILE A1187 " --> pdb=" O GLY A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1225 Processing helix chain 'B' and resid 3 through 20 removed outlier: 3.508A pdb=" N GLU B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.287A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.528A pdb=" N GLU B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 124 through 162 removed outlier: 4.589A pdb=" N GLU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 579 through 580 removed outlier: 3.853A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA3, first strand: chain 'A' and resid 521 through 522 removed outlier: 3.642A pdb=" N PHE A 521 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET A 746 " --> pdb=" O PHE A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=AA5, first strand: chain 'A' and resid 737 through 738 removed outlier: 3.658A pdb=" N ARG A 737 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 758 through 759 removed outlier: 3.691A pdb=" N HIS A 759 " --> pdb=" O VAL A 783 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 783 " --> pdb=" O HIS A 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 764 through 765 Processing sheet with id=AA8, first strand: chain 'A' and resid 828 through 833 removed outlier: 3.594A pdb=" N VAL A 842 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU A 839 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N SER A 855 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 841 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN A 853 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 843 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 858 through 862 removed outlier: 4.332A pdb=" N ILE A 868 " --> pdb=" O ASN A 861 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 922 through 925 removed outlier: 6.708A pdb=" N ILE A 922 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE A 996 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU A 924 " --> pdb=" O ILE A 996 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1047 through 1048 removed outlier: 3.844A pdb=" N LEU A1047 " --> pdb=" O TRP A1063 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A1063 " --> pdb=" O LEU A1047 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1072 through 1073 Processing sheet with id=AB4, first strand: chain 'A' and resid 1138 through 1140 455 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 3834 1.36 - 1.51: 4532 1.51 - 1.66: 3643 1.66 - 1.81: 19 1.81 - 1.96: 40 Bond restraints: 12068 Sorted by residual: bond pdb=" SD MET A 626 " pdb=" CE MET A 626 " ideal model delta sigma weight residual 1.791 1.963 -0.172 2.50e-02 1.60e+03 4.71e+01 bond pdb=" SD MET A 531 " pdb=" CE MET A 531 " ideal model delta sigma weight residual 1.791 1.963 -0.172 2.50e-02 1.60e+03 4.71e+01 bond pdb=" CG MET A 531 " pdb=" SD MET A 531 " ideal model delta sigma weight residual 1.803 1.964 -0.161 2.50e-02 1.60e+03 4.13e+01 bond pdb=" CG MET A 626 " pdb=" SD MET A 626 " ideal model delta sigma weight residual 1.803 1.963 -0.160 2.50e-02 1.60e+03 4.09e+01 bond pdb=" SD MET A 603 " pdb=" CE MET A 603 " ideal model delta sigma weight residual 1.791 1.950 -0.159 2.50e-02 1.60e+03 4.05e+01 ... (remaining 12063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 15278 2.10 - 4.20: 911 4.20 - 6.30: 112 6.30 - 8.39: 24 8.39 - 10.49: 11 Bond angle restraints: 16336 Sorted by residual: angle pdb=" N MET A 626 " pdb=" CA MET A 626 " pdb=" C MET A 626 " ideal model delta sigma weight residual 113.16 105.11 8.05 1.24e+00 6.50e-01 4.21e+01 angle pdb=" C PHE A 220 " pdb=" CA PHE A 220 " pdb=" CB PHE A 220 " ideal model delta sigma weight residual 109.29 119.28 -9.99 1.82e+00 3.02e-01 3.01e+01 angle pdb=" CA TRP B 100 " pdb=" C TRP B 100 " pdb=" O TRP B 100 " ideal model delta sigma weight residual 121.10 115.55 5.55 1.10e+00 8.26e-01 2.54e+01 angle pdb=" C GLU A 88 " pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 122.07 129.02 -6.95 1.43e+00 4.89e-01 2.36e+01 angle pdb=" C LYS A 265 " pdb=" N THR A 266 " pdb=" CA THR A 266 " ideal model delta sigma weight residual 121.54 130.70 -9.16 1.91e+00 2.74e-01 2.30e+01 ... (remaining 16331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 6974 32.09 - 64.19: 322 64.19 - 96.28: 23 96.28 - 128.37: 0 128.37 - 160.46: 1 Dihedral angle restraints: 7320 sinusoidal: 3287 harmonic: 4033 Sorted by residual: dihedral pdb=" O4' U G 16 " pdb=" C1' U G 16 " pdb=" N1 U G 16 " pdb=" C2 U G 16 " ideal model delta sinusoidal sigma weight residual 232.00 71.54 160.46 1 1.70e+01 3.46e-03 6.45e+01 dihedral pdb=" C ASP A 625 " pdb=" N ASP A 625 " pdb=" CA ASP A 625 " pdb=" CB ASP A 625 " ideal model delta harmonic sigma weight residual -122.60 -137.60 15.00 0 2.50e+00 1.60e-01 3.60e+01 dihedral pdb=" CA PHE A 863 " pdb=" C PHE A 863 " pdb=" N ASN A 864 " pdb=" CA ASN A 864 " ideal model delta harmonic sigma weight residual -180.00 -152.72 -27.28 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 7317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1514 0.098 - 0.196: 213 0.196 - 0.294: 15 0.294 - 0.392: 3 0.392 - 0.490: 2 Chirality restraints: 1747 Sorted by residual: chirality pdb=" CA ASP A 625 " pdb=" N ASP A 625 " pdb=" C ASP A 625 " pdb=" CB ASP A 625 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CB ILE A 798 " pdb=" CA ILE A 798 " pdb=" CG1 ILE A 798 " pdb=" CG2 ILE A 798 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CB ILE B 113 " pdb=" CA ILE B 113 " pdb=" CG1 ILE B 113 " pdb=" CG2 ILE B 113 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 1744 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 932 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LYS A 932 " -0.065 2.00e-02 2.50e+03 pdb=" O LYS A 932 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN A 933 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 717 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" C PRO A 717 " -0.046 2.00e-02 2.50e+03 pdb=" O PRO A 717 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A 718 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 128 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO A 129 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.037 5.00e-02 4.00e+02 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 218 2.59 - 3.17: 10101 3.17 - 3.75: 18647 3.75 - 4.32: 24597 4.32 - 4.90: 39086 Nonbonded interactions: 92649 Sorted by model distance: nonbonded pdb="MG MG G 101 " pdb=" O HOH G 201 " model vdw 2.014 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 203 " model vdw 2.031 2.170 nonbonded pdb=" OP2 A G 19 " pdb="MG MG A1301 " model vdw 2.033 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 204 " model vdw 2.035 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 205 " model vdw 2.045 2.170 ... (remaining 92644 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=1.00 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: 0.480 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.620 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4586 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 : 0.013 0.172 12068 Z= 0.604 Angle : 1.111 10.494 16336 Z= 0.648 Chirality : 0.071 0.490 1747 Planarity : 0.007 0.066 1999 Dihedral : 17.366 160.463 4720 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.70 % Favored : 88.86 % Rotamer: Outliers : 2.43 % Allowed : 13.30 % Favored : 84.27 % Cbeta Deviations : 0.38 % 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: -4.62 (0.17), residues: 1346 helix: -2.71 (0.14), residues: 634 sheet: -3.20 (0.44), residues: 112 loop : -3.38 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 508 TYR 0.029 0.003 TYR A 237 PHE 0.034 0.003 PHE A1161 TRP 0.037 0.003 TRP B 100 HIS 0.007 0.002 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.01332 (12068) covalent geometry : angle 1.11069 (16336) hydrogen bonds : bond 0.12095 ( 458) hydrogen bonds : angle 6.67492 ( 1308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 322 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 THR cc_start: 0.5928 (p) cc_final: 0.5475 (m) REVERT: A 189 ILE cc_start: 0.5144 (mm) cc_final: 0.4892 (tp) REVERT: A 230 THR cc_start: 0.5349 (t) cc_final: 0.4344 (p) REVERT: A 278 LYS cc_start: 0.6765 (ttmt) cc_final: 0.6404 (ttmm) REVERT: A 412 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6395 (tp30) REVERT: A 419 ILE cc_start: 0.7046 (tp) cc_final: 0.6729 (pt) REVERT: A 456 MET cc_start: 0.8104 (mtp) cc_final: 0.7698 (mtp) REVERT: A 525 PHE cc_start: 0.5230 (m-10) cc_final: 0.4612 (m-80) REVERT: A 796 LEU cc_start: 0.4979 (tt) cc_final: 0.4709 (tt) REVERT: A 899 LEU cc_start: 0.6186 (tp) cc_final: 0.5780 (tt) REVERT: A 1060 ILE cc_start: 0.5195 (mm) cc_final: 0.4111 (tt) REVERT: A 1088 GLU cc_start: 0.1620 (tm-30) cc_final: 0.0468 (tp30) REVERT: A 1131 MET cc_start: 0.6605 (mmm) cc_final: 0.6281 (mmm) REVERT: A 1174 ILE cc_start: 0.0898 (OUTLIER) cc_final: 0.0071 (mt) REVERT: A 1211 ILE cc_start: 0.3251 (OUTLIER) cc_final: 0.2972 (mp) REVERT: B 3 LYS cc_start: 0.6807 (tppt) cc_final: 0.6137 (tptp) REVERT: B 87 TYR cc_start: 0.5847 (m-80) cc_final: 0.5488 (m-80) outliers start: 30 outliers final: 6 residues processed: 347 average time/residue: 0.1291 time to fit residues: 60.5592 Evaluate side-chains 185 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 100 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.0070 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN A 509 ASN A 577 ASN A 633 HIS A 735 GLN A 849 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 ASN A1182 ASN B 20 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.199917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.154539 restraints weight = 20032.582| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 3.58 r_work: 0.3774 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12068 Z= 0.143 Angle : 0.671 10.687 16336 Z= 0.354 Chirality : 0.043 0.173 1747 Planarity : 0.004 0.043 1999 Dihedral : 12.288 154.324 1863 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.84 % Allowed : 17.68 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.21), residues: 1346 helix: -1.02 (0.19), residues: 641 sheet: -2.83 (0.47), residues: 105 loop : -2.76 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 102 TYR 0.020 0.002 TYR A 487 PHE 0.037 0.002 PHE A 931 TRP 0.007 0.001 TRP A1063 HIS 0.005 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00297 (12068) covalent geometry : angle 0.67131 (16336) hydrogen bonds : bond 0.03856 ( 458) hydrogen bonds : angle 5.03937 ( 1308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7383 (pp20) REVERT: A 119 PHE cc_start: 0.4632 (m-80) cc_final: 0.4139 (m-80) REVERT: A 120 LYS cc_start: 0.7409 (mmmt) cc_final: 0.6773 (ptpp) REVERT: A 152 THR cc_start: 0.5997 (t) cc_final: 0.5749 (m) REVERT: A 162 PHE cc_start: 0.7366 (m-80) cc_final: 0.7116 (m-80) REVERT: A 230 THR cc_start: 0.5094 (t) cc_final: 0.4847 (p) REVERT: A 272 LYS cc_start: 0.6307 (mttp) cc_final: 0.5917 (ttmm) REVERT: A 412 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6859 (tp30) REVERT: A 469 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.6582 (m-10) REVERT: A 494 TYR cc_start: 0.5350 (t80) cc_final: 0.5096 (t80) REVERT: A 559 ASP cc_start: 0.7132 (m-30) cc_final: 0.5742 (m-30) REVERT: A 597 PHE cc_start: 0.4310 (m-10) cc_final: 0.3885 (m-80) REVERT: A 646 TYR cc_start: 0.6146 (t80) cc_final: 0.5355 (t80) REVERT: A 735 GLN cc_start: 0.5955 (OUTLIER) cc_final: 0.5662 (mp-120) REVERT: B 3 LYS cc_start: 0.6527 (tppt) cc_final: 0.5938 (tptp) REVERT: B 15 LYS cc_start: 0.8356 (tppt) cc_final: 0.8055 (tppt) REVERT: B 18 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7687 (mm-40) REVERT: B 100 TRP cc_start: 0.5922 (OUTLIER) cc_final: 0.5454 (p90) REVERT: B 155 ARG cc_start: 0.5872 (mmm-85) cc_final: 0.4823 (tpp80) outliers start: 35 outliers final: 15 residues processed: 260 average time/residue: 0.1048 time to fit residues: 38.7290 Evaluate side-chains 191 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 100 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 95 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 513 GLN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN ** A 873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.172380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.125833 restraints weight = 19605.088| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.31 r_work: 0.3488 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 1.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 12068 Z= 0.320 Angle : 0.923 9.623 16336 Z= 0.487 Chirality : 0.051 0.296 1747 Planarity : 0.006 0.092 1999 Dihedral : 12.917 157.982 1854 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 5.11 % Allowed : 18.90 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.02 (0.21), residues: 1346 helix: -0.98 (0.19), residues: 626 sheet: -3.39 (0.39), residues: 112 loop : -2.83 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 508 TYR 0.028 0.003 TYR A 653 PHE 0.025 0.003 PHE A1127 TRP 0.024 0.003 TRP A 355 HIS 0.008 0.002 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00703 (12068) covalent geometry : angle 0.92300 (16336) hydrogen bonds : bond 0.05522 ( 458) hydrogen bonds : angle 5.67106 ( 1308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7334 (ptpp) REVERT: A 147 PHE cc_start: 0.6634 (t80) cc_final: 0.6339 (t80) REVERT: A 159 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6747 (tm-30) REVERT: A 220 PHE cc_start: 0.7488 (m-80) cc_final: 0.7273 (m-80) REVERT: A 238 ASN cc_start: 0.7667 (m-40) cc_final: 0.7111 (m110) REVERT: A 325 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6473 (t80) REVERT: A 412 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7518 (tp30) REVERT: A 448 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8515 (mppt) REVERT: A 466 PHE cc_start: 0.8386 (t80) cc_final: 0.7884 (t80) REVERT: A 467 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 471 LYS cc_start: 0.7820 (tppt) cc_final: 0.7376 (mtpp) REVERT: A 494 TYR cc_start: 0.6836 (t80) cc_final: 0.6528 (t80) REVERT: A 531 MET cc_start: 0.8415 (ttm) cc_final: 0.8052 (mtp) REVERT: A 645 ARG cc_start: 0.8152 (mtp180) cc_final: 0.7874 (mtm-85) REVERT: A 653 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.6559 (m-10) REVERT: A 654 ASP cc_start: 0.8346 (t0) cc_final: 0.8061 (m-30) REVERT: A 692 LYS cc_start: 0.8369 (ttpp) cc_final: 0.8034 (tptt) REVERT: A 693 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7744 (tt) REVERT: A 708 ASP cc_start: 0.8676 (t70) cc_final: 0.8357 (t70) REVERT: A 728 PHE cc_start: 0.8358 (m-80) cc_final: 0.8031 (m-80) REVERT: A 755 GLU cc_start: 0.8349 (pm20) cc_final: 0.8084 (pm20) REVERT: A 795 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8074 (mt-10) REVERT: A 858 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7611 (mm-30) REVERT: A 900 LYS cc_start: 0.8977 (mttp) cc_final: 0.8706 (mmtm) REVERT: A 999 TRP cc_start: 0.7724 (m-10) cc_final: 0.7297 (m-10) REVERT: A 1086 TRP cc_start: 0.6770 (t60) cc_final: 0.6369 (t60) REVERT: A 1149 PHE cc_start: 0.6759 (p90) cc_final: 0.6433 (p90) REVERT: A 1163 ASP cc_start: 0.7536 (m-30) cc_final: 0.6926 (t0) REVERT: A 1217 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: B 15 LYS cc_start: 0.8449 (tppt) cc_final: 0.8120 (tppt) REVERT: B 29 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5486 (pm20) REVERT: B 56 SER cc_start: 0.8038 (OUTLIER) cc_final: 0.7676 (p) REVERT: B 100 TRP cc_start: 0.7651 (OUTLIER) cc_final: 0.6767 (p90) REVERT: B 121 ASP cc_start: 0.6732 (t70) cc_final: 0.6166 (p0) REVERT: B 130 LEU cc_start: 0.8270 (mm) cc_final: 0.8051 (mm) REVERT: B 156 ARG cc_start: 0.6817 (tmm-80) cc_final: 0.6430 (ttt180) outliers start: 63 outliers final: 19 residues processed: 309 average time/residue: 0.1072 time to fit residues: 46.4152 Evaluate side-chains 213 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 1162 TYR Chi-restraints excluded: chain A residue 1217 GLU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 101 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 120 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN A1172 ASN B 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.163874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.115791 restraints weight = 19354.988| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.29 r_work: 0.3320 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 1.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12068 Z= 0.237 Angle : 0.740 8.645 16336 Z= 0.392 Chirality : 0.046 0.223 1747 Planarity : 0.005 0.048 1999 Dihedral : 12.288 166.627 1849 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.27 % Allowed : 21.33 % Favored : 73.40 % 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: -2.65 (0.22), residues: 1346 helix: -0.60 (0.20), residues: 642 sheet: -2.96 (0.42), residues: 120 loop : -2.84 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 385 TYR 0.034 0.002 TYR A 616 PHE 0.038 0.002 PHE A1198 TRP 0.015 0.002 TRP A 534 HIS 0.006 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00538 (12068) covalent geometry : angle 0.74003 (16336) hydrogen bonds : bond 0.04422 ( 458) hydrogen bonds : angle 5.15392 ( 1308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 238 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 THR cc_start: 0.9599 (OUTLIER) cc_final: 0.9348 (p) REVERT: A 159 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6794 (tm-30) REVERT: A 178 GLU cc_start: 0.8071 (tp30) cc_final: 0.7745 (tp30) REVERT: A 220 PHE cc_start: 0.7288 (m-80) cc_final: 0.7048 (m-80) REVERT: A 238 ASN cc_start: 0.7903 (m-40) cc_final: 0.7320 (m110) REVERT: A 325 PHE cc_start: 0.6841 (OUTLIER) cc_final: 0.6264 (t80) REVERT: A 350 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8088 (t0) REVERT: A 423 ASP cc_start: 0.8558 (p0) cc_final: 0.8291 (p0) REVERT: A 448 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8559 (mppt) REVERT: A 466 PHE cc_start: 0.8634 (t80) cc_final: 0.8013 (t80) REVERT: A 467 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 471 LYS cc_start: 0.7917 (tppt) cc_final: 0.7444 (mtpp) REVERT: A 494 TYR cc_start: 0.7053 (t80) cc_final: 0.6425 (t80) REVERT: A 531 MET cc_start: 0.8431 (ttm) cc_final: 0.8193 (mtp) REVERT: A 539 GLU cc_start: 0.7402 (pm20) cc_final: 0.7076 (tt0) REVERT: A 562 TYR cc_start: 0.8190 (m-80) cc_final: 0.7738 (m-80) REVERT: A 565 CYS cc_start: 0.8121 (m) cc_final: 0.7871 (m) REVERT: A 600 LYS cc_start: 0.5274 (OUTLIER) cc_final: 0.5032 (mtmm) REVERT: A 603 MET cc_start: 0.7837 (mtp) cc_final: 0.7293 (mtm) REVERT: A 626 MET cc_start: 0.6150 (mmp) cc_final: 0.5829 (mmt) REVERT: A 659 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6043 (mp0) REVERT: A 663 TYR cc_start: 0.7834 (m-80) cc_final: 0.6592 (m-80) REVERT: A 836 ARG cc_start: 0.8046 (tpp-160) cc_final: 0.7832 (mpt180) REVERT: A 858 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 861 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7500 (p0) REVERT: A 867 ARG cc_start: 0.8380 (ptp-110) cc_final: 0.7862 (mtp85) REVERT: A 999 TRP cc_start: 0.7654 (m-10) cc_final: 0.7228 (m-10) REVERT: A 1134 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.5836 (mmp) REVERT: A 1149 PHE cc_start: 0.7346 (p90) cc_final: 0.6957 (p90) REVERT: A 1163 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7155 (t0) REVERT: B 16 LYS cc_start: 0.5759 (OUTLIER) cc_final: 0.5261 (mtpp) REVERT: B 17 MET cc_start: 0.7914 (tpt) cc_final: 0.7456 (mmm) REVERT: B 19 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6964 (tm-30) REVERT: B 25 THR cc_start: 0.6190 (m) cc_final: 0.5837 (p) REVERT: B 76 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8227 (tm-30) REVERT: B 100 TRP cc_start: 0.7588 (OUTLIER) cc_final: 0.6522 (p90) REVERT: B 121 ASP cc_start: 0.7292 (t70) cc_final: 0.6699 (p0) REVERT: B 145 GLU cc_start: 0.8456 (tt0) cc_final: 0.8197 (tm-30) REVERT: B 152 LYS cc_start: 0.7294 (ttmm) cc_final: 0.7071 (mtpt) REVERT: B 156 ARG cc_start: 0.6894 (tmm-80) cc_final: 0.6443 (ttt180) outliers start: 65 outliers final: 27 residues processed: 288 average time/residue: 0.1195 time to fit residues: 48.1353 Evaluate side-chains 228 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1163 ASP Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain A residue 1193 TRP Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 154 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 11 optimal weight: 7.9990 chunk 124 optimal weight: 0.0470 chunk 85 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 80 optimal weight: 0.4980 chunk 8 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 735 GLN A 861 ASN A1172 ASN B 67 GLN B 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.167689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120462 restraints weight = 19112.690| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.28 r_work: 0.3398 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 1.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12068 Z= 0.126 Angle : 0.628 9.689 16336 Z= 0.330 Chirality : 0.042 0.206 1747 Planarity : 0.004 0.040 1999 Dihedral : 11.900 169.562 1849 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.33 % Allowed : 24.33 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.22), residues: 1346 helix: -0.10 (0.21), residues: 639 sheet: -2.74 (0.43), residues: 119 loop : -2.56 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 645 TYR 0.014 0.001 TYR B 136 PHE 0.027 0.001 PHE A1198 TRP 0.018 0.001 TRP A1193 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00286 (12068) covalent geometry : angle 0.62757 (16336) hydrogen bonds : bond 0.03452 ( 458) hydrogen bonds : angle 4.79832 ( 1308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 THR cc_start: 0.9550 (OUTLIER) cc_final: 0.9342 (p) REVERT: A 120 LYS cc_start: 0.7858 (mmmt) cc_final: 0.7464 (ptpp) REVERT: A 159 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6712 (tt0) REVERT: A 220 PHE cc_start: 0.7353 (m-80) cc_final: 0.6842 (m-80) REVERT: A 224 PHE cc_start: 0.7486 (m-80) cc_final: 0.7215 (m-80) REVERT: A 257 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8222 (pt0) REVERT: A 325 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.5927 (t80) REVERT: A 350 ASP cc_start: 0.8228 (m-30) cc_final: 0.7994 (t70) REVERT: A 399 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 423 ASP cc_start: 0.8611 (p0) cc_final: 0.8314 (p0) REVERT: A 448 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8636 (mppt) REVERT: A 466 PHE cc_start: 0.8650 (t80) cc_final: 0.8073 (t80) REVERT: A 467 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 471 LYS cc_start: 0.7952 (tppt) cc_final: 0.7508 (mtpp) REVERT: A 539 GLU cc_start: 0.7349 (pm20) cc_final: 0.7084 (tt0) REVERT: A 562 TYR cc_start: 0.8078 (m-80) cc_final: 0.7407 (m-80) REVERT: A 571 LYS cc_start: 0.7786 (tmtt) cc_final: 0.7496 (tmtt) REVERT: A 603 MET cc_start: 0.7871 (mtp) cc_final: 0.7500 (mtm) REVERT: A 663 TYR cc_start: 0.7873 (m-80) cc_final: 0.7491 (m-80) REVERT: A 670 TYR cc_start: 0.8516 (m-10) cc_final: 0.8187 (m-10) REVERT: A 708 ASP cc_start: 0.8698 (t70) cc_final: 0.8352 (t0) REVERT: A 811 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7773 (tttm) REVERT: A 836 ARG cc_start: 0.8070 (tpp-160) cc_final: 0.7851 (mpt180) REVERT: A 842 VAL cc_start: 0.9656 (p) cc_final: 0.9417 (m) REVERT: A 861 ASN cc_start: 0.7746 (OUTLIER) cc_final: 0.7522 (p0) REVERT: A 867 ARG cc_start: 0.8347 (ptp-110) cc_final: 0.7913 (mtp85) REVERT: A 1086 TRP cc_start: 0.6282 (t60) cc_final: 0.5726 (t60) REVERT: A 1128 MET cc_start: 0.6303 (ttm) cc_final: 0.5591 (ppp) REVERT: A 1135 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6891 (mp) REVERT: A 1141 ILE cc_start: 0.7449 (pt) cc_final: 0.7238 (pt) REVERT: A 1149 PHE cc_start: 0.6910 (p90) cc_final: 0.6669 (p90) REVERT: A 1163 ASP cc_start: 0.7408 (m-30) cc_final: 0.7112 (t0) REVERT: A 1217 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 17 MET cc_start: 0.7968 (tpt) cc_final: 0.7728 (mmm) REVERT: B 25 THR cc_start: 0.6281 (m) cc_final: 0.5934 (p) REVERT: B 76 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8163 (tm-30) REVERT: B 100 TRP cc_start: 0.7675 (OUTLIER) cc_final: 0.6087 (p90) REVERT: B 121 ASP cc_start: 0.7383 (t70) cc_final: 0.6806 (p0) REVERT: B 122 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6751 (mt) REVERT: B 136 TYR cc_start: 0.8053 (t80) cc_final: 0.7805 (t80) REVERT: B 156 ARG cc_start: 0.6926 (tmm-80) cc_final: 0.6674 (ttt180) outliers start: 41 outliers final: 21 residues processed: 254 average time/residue: 0.1128 time to fit residues: 39.9022 Evaluate side-chains 217 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 101 PHE Chi-restraints excluded: chain B residue 122 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 99 optimal weight: 0.0470 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 735 GLN A 861 ASN A 862 ASN A1172 ASN A1186 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.161734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.116449 restraints weight = 19192.907| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.31 r_work: 0.3291 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 1.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12068 Z= 0.173 Angle : 0.677 11.509 16336 Z= 0.355 Chirality : 0.044 0.234 1747 Planarity : 0.004 0.040 1999 Dihedral : 11.938 171.858 1849 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.46 % Allowed : 24.74 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.22), residues: 1346 helix: -0.05 (0.21), residues: 638 sheet: -2.60 (0.47), residues: 109 loop : -2.41 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 935 TYR 0.022 0.002 TYR A1068 PHE 0.034 0.002 PHE A1198 TRP 0.014 0.001 TRP A 355 HIS 0.005 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00394 (12068) covalent geometry : angle 0.67726 (16336) hydrogen bonds : bond 0.03798 ( 458) hydrogen bonds : angle 4.87793 ( 1308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 THR cc_start: 0.9611 (OUTLIER) cc_final: 0.9377 (p) REVERT: A 159 GLU cc_start: 0.7309 (tm-30) cc_final: 0.7042 (tt0) REVERT: A 187 MET cc_start: 0.4909 (tpp) cc_final: 0.4306 (ttp) REVERT: A 220 PHE cc_start: 0.7219 (m-80) cc_final: 0.6459 (m-80) REVERT: A 238 ASN cc_start: 0.7817 (m-40) cc_final: 0.7189 (m110) REVERT: A 257 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8187 (pt0) REVERT: A 325 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.6259 (t80) REVERT: A 350 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7604 (t0) REVERT: A 362 TRP cc_start: 0.6881 (t60) cc_final: 0.6503 (t60) REVERT: A 399 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 414 LEU cc_start: 0.7991 (mt) cc_final: 0.7676 (mt) REVERT: A 423 ASP cc_start: 0.8635 (p0) cc_final: 0.8352 (p0) REVERT: A 448 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8659 (mppt) REVERT: A 466 PHE cc_start: 0.8678 (t80) cc_final: 0.8052 (t80) REVERT: A 467 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 471 LYS cc_start: 0.7992 (tppt) cc_final: 0.7603 (mtpp) REVERT: A 494 TYR cc_start: 0.7207 (t80) cc_final: 0.6935 (t80) REVERT: A 539 GLU cc_start: 0.7213 (pm20) cc_final: 0.6987 (tt0) REVERT: A 562 TYR cc_start: 0.8138 (m-80) cc_final: 0.7612 (m-80) REVERT: A 571 LYS cc_start: 0.7722 (tmtt) cc_final: 0.7465 (tmtt) REVERT: A 603 MET cc_start: 0.8160 (mtp) cc_final: 0.7822 (mtm) REVERT: A 630 ASN cc_start: 0.7802 (m-40) cc_final: 0.7580 (t0) REVERT: A 653 TYR cc_start: 0.6704 (m-10) cc_final: 0.6373 (m-10) REVERT: A 670 TYR cc_start: 0.8845 (m-10) cc_final: 0.8618 (m-10) REVERT: A 708 ASP cc_start: 0.8397 (t70) cc_final: 0.8141 (t70) REVERT: A 836 ARG cc_start: 0.8234 (tpp-160) cc_final: 0.8013 (mpt180) REVERT: A 867 ARG cc_start: 0.8342 (ptp-110) cc_final: 0.8045 (mtp85) REVERT: A 949 MET cc_start: 0.8598 (tpp) cc_final: 0.8261 (mmt) REVERT: A 992 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.5888 (t80) REVERT: A 1163 ASP cc_start: 0.7404 (m-30) cc_final: 0.7178 (t0) REVERT: A 1217 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7924 (mt-10) REVERT: B 17 MET cc_start: 0.8035 (tpt) cc_final: 0.7756 (mmm) REVERT: B 50 SER cc_start: 0.8417 (t) cc_final: 0.8183 (t) REVERT: B 76 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8128 (tm-30) REVERT: B 94 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8194 (p0) REVERT: B 100 TRP cc_start: 0.7809 (OUTLIER) cc_final: 0.6213 (p90) REVERT: B 121 ASP cc_start: 0.7568 (t70) cc_final: 0.7025 (p0) REVERT: B 122 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7363 (mt) REVERT: B 148 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7786 (mm110) REVERT: B 156 ARG cc_start: 0.7306 (tmm-80) cc_final: 0.6895 (ttt180) outliers start: 55 outliers final: 30 residues processed: 252 average time/residue: 0.1056 time to fit residues: 38.1763 Evaluate side-chains 221 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 735 GLN Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain A residue 1193 TRP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 99 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 468 ASN A 861 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114551 restraints weight = 19511.291| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 4.90 r_work: 0.3107 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 1.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 12068 Z= 0.317 Angle : 0.831 11.693 16336 Z= 0.442 Chirality : 0.051 0.270 1747 Planarity : 0.005 0.047 1999 Dihedral : 12.566 174.276 1849 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.95 % Allowed : 25.14 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.40 (0.22), residues: 1346 helix: -0.46 (0.20), residues: 649 sheet: -2.82 (0.44), residues: 121 loop : -2.64 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 935 TYR 0.033 0.003 TYR A1068 PHE 0.036 0.002 PHE A1198 TRP 0.034 0.003 TRP A 355 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00721 (12068) covalent geometry : angle 0.83141 (16336) hydrogen bonds : bond 0.05011 ( 458) hydrogen bonds : angle 5.44455 ( 1308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 203 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9369 (p) REVERT: A 17 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8931 (mt) REVERT: A 35 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8608 (mmm-85) REVERT: A 116 LYS cc_start: 0.9242 (mmmt) cc_final: 0.8724 (pttp) REVERT: A 174 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7718 (mmm-85) REVERT: A 187 MET cc_start: 0.5663 (tpp) cc_final: 0.5106 (ttp) REVERT: A 350 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.7969 (t0) REVERT: A 423 ASP cc_start: 0.8596 (p0) cc_final: 0.8334 (p0) REVERT: A 467 GLU cc_start: 0.8508 (tm-30) cc_final: 0.7932 (tm-30) REVERT: A 471 LYS cc_start: 0.8181 (tppt) cc_final: 0.7858 (mmmm) REVERT: A 571 LYS cc_start: 0.7958 (tmtt) cc_final: 0.7561 (tmtt) REVERT: A 592 MET cc_start: 0.7958 (tpt) cc_final: 0.7298 (tpt) REVERT: A 617 LYS cc_start: 0.8688 (tttm) cc_final: 0.8301 (tmtt) REVERT: A 628 ASN cc_start: 0.7352 (t0) cc_final: 0.6724 (m-40) REVERT: A 629 LEU cc_start: 0.7940 (mp) cc_final: 0.7433 (mp) REVERT: A 630 ASN cc_start: 0.8283 (m-40) cc_final: 0.7897 (t0) REVERT: A 656 ASN cc_start: 0.8800 (m-40) cc_final: 0.8207 (p0) REVERT: A 688 LYS cc_start: 0.7471 (pttt) cc_final: 0.7120 (tptt) REVERT: A 708 ASP cc_start: 0.8682 (t70) cc_final: 0.8458 (t70) REVERT: A 836 ARG cc_start: 0.8393 (tpp-160) cc_final: 0.8003 (mmp80) REVERT: A 858 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7436 (pt0) REVERT: A 861 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7837 (p0) REVERT: A 965 CYS cc_start: 0.8462 (t) cc_final: 0.8249 (p) REVERT: A 1054 ARG cc_start: 0.7706 (mpt180) cc_final: 0.7033 (mmm-85) REVERT: A 1126 SER cc_start: 0.9017 (t) cc_final: 0.8658 (p) REVERT: A 1128 MET cc_start: 0.6987 (ttm) cc_final: 0.6101 (ppp) REVERT: A 1131 MET cc_start: 0.8234 (mmm) cc_final: 0.7348 (tpp) REVERT: A 1134 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7654 (tpp) REVERT: A 1135 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8384 (mm) REVERT: A 1163 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7398 (t0) REVERT: B 16 LYS cc_start: 0.5874 (OUTLIER) cc_final: 0.5184 (mtpp) REVERT: B 17 MET cc_start: 0.8089 (tpt) cc_final: 0.7728 (mmm) REVERT: B 76 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8219 (tm-30) REVERT: B 100 TRP cc_start: 0.7958 (OUTLIER) cc_final: 0.6078 (p90) REVERT: B 121 ASP cc_start: 0.8209 (t70) cc_final: 0.7557 (p0) REVERT: B 160 GLU cc_start: 0.8197 (tp30) cc_final: 0.7848 (tt0) outliers start: 61 outliers final: 34 residues processed: 249 average time/residue: 0.1121 time to fit residues: 39.5846 Evaluate side-chains 222 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1163 ASP Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 130 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 55 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 468 ASN A 618 ASN A 861 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.160019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114179 restraints weight = 19145.240| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.20 r_work: 0.3289 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 1.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.138 12068 Z= 0.134 Angle : 0.692 11.188 16336 Z= 0.358 Chirality : 0.044 0.220 1747 Planarity : 0.003 0.036 1999 Dihedral : 11.975 176.912 1849 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.41 % Allowed : 26.93 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.85 (0.22), residues: 1346 helix: -0.07 (0.20), residues: 649 sheet: -2.29 (0.47), residues: 114 loop : -2.36 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 935 TYR 0.021 0.001 TYR A 605 PHE 0.031 0.002 PHE A1149 TRP 0.009 0.001 TRP A 362 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00319 (12068) covalent geometry : angle 0.69173 (16336) hydrogen bonds : bond 0.03569 ( 458) hydrogen bonds : angle 4.93545 ( 1308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9307 (mmmt) cc_final: 0.8744 (pttp) REVERT: A 187 MET cc_start: 0.5603 (tpp) cc_final: 0.4870 (ttp) REVERT: A 238 ASN cc_start: 0.7901 (m-40) cc_final: 0.7253 (m110) REVERT: A 257 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8187 (pt0) REVERT: A 307 THR cc_start: 0.8877 (t) cc_final: 0.8622 (p) REVERT: A 350 ASP cc_start: 0.8410 (m-30) cc_final: 0.8003 (t0) REVERT: A 359 ARG cc_start: 0.7896 (tmt-80) cc_final: 0.7589 (tpt90) REVERT: A 399 GLN cc_start: 0.8261 (tt0) cc_final: 0.7985 (pt0) REVERT: A 423 ASP cc_start: 0.8573 (p0) cc_final: 0.8129 (m-30) REVERT: A 494 TYR cc_start: 0.7257 (t80) cc_final: 0.6924 (t80) REVERT: A 539 GLU cc_start: 0.7704 (pm20) cc_final: 0.7057 (tt0) REVERT: A 562 TYR cc_start: 0.8293 (m-80) cc_final: 0.7806 (m-80) REVERT: A 571 LYS cc_start: 0.7769 (tmtt) cc_final: 0.7456 (tmtt) REVERT: A 592 MET cc_start: 0.7434 (tpt) cc_final: 0.7054 (tpt) REVERT: A 628 ASN cc_start: 0.7400 (t0) cc_final: 0.7103 (t0) REVERT: A 653 TYR cc_start: 0.7099 (m-10) cc_final: 0.6691 (m-10) REVERT: A 656 ASN cc_start: 0.8685 (m-40) cc_final: 0.8212 (p0) REVERT: A 688 LYS cc_start: 0.7171 (pttt) cc_final: 0.6818 (tptt) REVERT: A 795 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8372 (mt-10) REVERT: A 808 ASN cc_start: 0.8542 (t0) cc_final: 0.8151 (t0) REVERT: A 949 MET cc_start: 0.8494 (tpp) cc_final: 0.8187 (mmt) REVERT: A 992 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.6233 (t80) REVERT: A 1026 LYS cc_start: 0.8489 (mttp) cc_final: 0.8148 (ttpt) REVERT: A 1044 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6153 (tm-30) REVERT: A 1054 ARG cc_start: 0.7777 (mpt180) cc_final: 0.7083 (mmm-85) REVERT: A 1126 SER cc_start: 0.9035 (t) cc_final: 0.8662 (p) REVERT: A 1131 MET cc_start: 0.7997 (mmm) cc_final: 0.7348 (tpp) REVERT: A 1134 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7963 (tpp) REVERT: B 16 LYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5335 (mtpp) REVERT: B 17 MET cc_start: 0.7982 (tpt) cc_final: 0.7577 (mmm) REVERT: B 100 TRP cc_start: 0.7643 (OUTLIER) cc_final: 0.5244 (p90) REVERT: B 121 ASP cc_start: 0.8038 (t70) cc_final: 0.7463 (p0) REVERT: B 132 TYR cc_start: 0.8553 (t80) cc_final: 0.8205 (t80) REVERT: B 160 GLU cc_start: 0.8230 (tp30) cc_final: 0.7883 (tt0) REVERT: B 164 GLN cc_start: 0.6383 (pm20) cc_final: 0.6158 (pm20) outliers start: 42 outliers final: 25 residues processed: 229 average time/residue: 0.1060 time to fit residues: 34.6298 Evaluate side-chains 208 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 100 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 618 ASN A 861 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.158565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112954 restraints weight = 19054.795| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.17 r_work: 0.3292 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 1.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 12068 Z= 0.154 Angle : 0.687 11.161 16336 Z= 0.359 Chirality : 0.045 0.232 1747 Planarity : 0.003 0.042 1999 Dihedral : 11.924 178.792 1849 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.41 % Allowed : 27.74 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.74 (0.23), residues: 1346 helix: -0.02 (0.21), residues: 651 sheet: -2.16 (0.47), residues: 114 loop : -2.26 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 935 TYR 0.017 0.001 TYR A1068 PHE 0.028 0.002 PHE A1149 TRP 0.039 0.002 TRP A1193 HIS 0.003 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00364 (12068) covalent geometry : angle 0.68733 (16336) hydrogen bonds : bond 0.03662 ( 458) hydrogen bonds : angle 4.96336 ( 1308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9299 (mmmt) cc_final: 0.8698 (pttp) REVERT: A 187 MET cc_start: 0.5655 (tpp) cc_final: 0.5038 (ttp) REVERT: A 238 ASN cc_start: 0.7899 (m-40) cc_final: 0.7245 (m110) REVERT: A 257 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8186 (pt0) REVERT: A 307 THR cc_start: 0.8883 (t) cc_final: 0.8639 (p) REVERT: A 350 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8103 (t70) REVERT: A 423 ASP cc_start: 0.8661 (p0) cc_final: 0.8188 (m-30) REVERT: A 539 GLU cc_start: 0.7838 (pm20) cc_final: 0.7222 (tt0) REVERT: A 562 TYR cc_start: 0.8292 (m-80) cc_final: 0.7760 (m-80) REVERT: A 571 LYS cc_start: 0.7792 (tmtt) cc_final: 0.7485 (tmtt) REVERT: A 592 MET cc_start: 0.7724 (tpt) cc_final: 0.7063 (tpt) REVERT: A 656 ASN cc_start: 0.8663 (m-40) cc_final: 0.8169 (p0) REVERT: A 688 LYS cc_start: 0.7195 (pttt) cc_final: 0.6864 (tptt) REVERT: A 808 ASN cc_start: 0.8527 (t0) cc_final: 0.8180 (t0) REVERT: A 835 GLU cc_start: 0.7722 (pm20) cc_final: 0.5936 (pm20) REVERT: A 992 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.6344 (t80) REVERT: A 1026 LYS cc_start: 0.8537 (mttp) cc_final: 0.8170 (ttpt) REVERT: A 1044 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6877 (tt0) REVERT: A 1054 ARG cc_start: 0.7772 (mpt180) cc_final: 0.7019 (mmm-85) REVERT: A 1126 SER cc_start: 0.9109 (t) cc_final: 0.8736 (p) REVERT: A 1128 MET cc_start: 0.7169 (ptp) cc_final: 0.6478 (ppp) REVERT: A 1134 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7837 (tpp) REVERT: B 16 LYS cc_start: 0.6069 (OUTLIER) cc_final: 0.5458 (mtpp) REVERT: B 17 MET cc_start: 0.8063 (tpt) cc_final: 0.7628 (mmm) REVERT: B 82 ILE cc_start: 0.7497 (mm) cc_final: 0.7116 (mt) REVERT: B 100 TRP cc_start: 0.7639 (OUTLIER) cc_final: 0.5167 (p90) REVERT: B 121 ASP cc_start: 0.8001 (t70) cc_final: 0.7483 (p0) REVERT: B 132 TYR cc_start: 0.8560 (t80) cc_final: 0.8159 (t80) REVERT: B 160 GLU cc_start: 0.8277 (tp30) cc_final: 0.7827 (tt0) outliers start: 42 outliers final: 32 residues processed: 219 average time/residue: 0.1094 time to fit residues: 34.5484 Evaluate side-chains 215 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 67 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 128 optimal weight: 0.0770 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN A 618 ASN A 861 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.154994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117327 restraints weight = 19277.729| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 4.44 r_work: 0.3147 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 1.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12068 Z= 0.222 Angle : 0.749 11.484 16336 Z= 0.392 Chirality : 0.047 0.234 1747 Planarity : 0.004 0.041 1999 Dihedral : 12.084 178.368 1849 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.36 % Favored : 92.57 % Rotamer: Outliers : 3.16 % Allowed : 27.90 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.89 (0.22), residues: 1346 helix: -0.14 (0.21), residues: 660 sheet: -2.29 (0.46), residues: 121 loop : -2.35 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 935 TYR 0.024 0.002 TYR A1068 PHE 0.028 0.002 PHE A 225 TRP 0.045 0.002 TRP A1193 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00512 (12068) covalent geometry : angle 0.74894 (16336) hydrogen bonds : bond 0.04174 ( 458) hydrogen bonds : angle 5.19712 ( 1308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9282 (mmmt) cc_final: 0.8768 (pttp) REVERT: A 187 MET cc_start: 0.5761 (tpp) cc_final: 0.5176 (ttp) REVERT: A 307 THR cc_start: 0.8889 (t) cc_final: 0.8654 (p) REVERT: A 350 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8043 (t0) REVERT: A 423 ASP cc_start: 0.8676 (p0) cc_final: 0.8294 (m-30) REVERT: A 471 LYS cc_start: 0.7994 (tppt) cc_final: 0.7675 (mmmm) REVERT: A 498 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7936 (mm) REVERT: A 539 GLU cc_start: 0.7998 (pm20) cc_final: 0.7384 (tt0) REVERT: A 571 LYS cc_start: 0.7895 (tmtt) cc_final: 0.7378 (tmtt) REVERT: A 617 LYS cc_start: 0.8773 (tttm) cc_final: 0.8319 (tmtt) REVERT: A 628 ASN cc_start: 0.7563 (t0) cc_final: 0.6814 (m-40) REVERT: A 656 ASN cc_start: 0.8708 (m-40) cc_final: 0.8200 (p0) REVERT: A 722 MET cc_start: 0.8349 (ttm) cc_final: 0.7995 (mtt) REVERT: A 808 ASN cc_start: 0.8536 (t0) cc_final: 0.8160 (t0) REVERT: A 992 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.6449 (t80) REVERT: A 1044 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6833 (tt0) REVERT: A 1054 ARG cc_start: 0.7877 (mpt180) cc_final: 0.7141 (mmm-85) REVERT: A 1126 SER cc_start: 0.9150 (t) cc_final: 0.8766 (p) REVERT: A 1128 MET cc_start: 0.7486 (ptp) cc_final: 0.6729 (ppp) REVERT: A 1131 MET cc_start: 0.7159 (mmm) cc_final: 0.6286 (tpp) REVERT: A 1134 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7854 (tpp) REVERT: B 16 LYS cc_start: 0.5944 (OUTLIER) cc_final: 0.5427 (mtpp) REVERT: B 82 ILE cc_start: 0.7777 (mm) cc_final: 0.7490 (mt) REVERT: B 100 TRP cc_start: 0.7841 (OUTLIER) cc_final: 0.5831 (p90) REVERT: B 121 ASP cc_start: 0.8077 (t70) cc_final: 0.7478 (p0) REVERT: B 160 GLU cc_start: 0.8313 (tp30) cc_final: 0.7872 (tt0) outliers start: 39 outliers final: 33 residues processed: 217 average time/residue: 0.1081 time to fit residues: 33.3902 Evaluate side-chains 214 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 325 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1134 MET Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 306 ASN A 618 ASN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.158835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113061 restraints weight = 19141.470| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.17 r_work: 0.3267 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 1.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 12068 Z= 0.147 Angle : 0.698 12.584 16336 Z= 0.363 Chirality : 0.044 0.231 1747 Planarity : 0.003 0.037 1999 Dihedral : 11.935 179.412 1849 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.08 % Allowed : 28.63 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.23), residues: 1346 helix: 0.07 (0.21), residues: 650 sheet: -2.08 (0.48), residues: 114 loop : -2.21 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 385 TYR 0.029 0.002 TYR A 670 PHE 0.026 0.001 PHE A1149 TRP 0.044 0.002 TRP A1193 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00340 (12068) covalent geometry : angle 0.69816 (16336) hydrogen bonds : bond 0.03639 ( 458) hydrogen bonds : angle 5.03672 ( 1308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3149.89 seconds wall clock time: 54 minutes 37.51 seconds (3277.51 seconds total)