Starting phenix.real_space_refine on Fri Sep 11 22:22:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nmd_0447/09_2026/6nmd_0447.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nmd_0447/09_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_0447/09_2026/6nmd_0447.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nmd_0447/09_2026/6nmd_0447.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nmd_0447/09_2026/6nmd_0447.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nmd_0447/09_2026/6nmd_0447.cif" model { file = "/net/cci-nas-00/data/ceres_data/6nmd_0447/09_2026/6nmd_0447.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nmd_0447/09_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 2.79, per 1000 atoms: 0.24 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: 0.93 Conformation dependent library (CDL) restraints added in 533.6 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: 1.25 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: 2.09 Time building geometry restraints manager: 1.26 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: 15209 2.10 - 4.20: 975 4.20 - 6.30: 117 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 - 17.75: 6145 17.75 - 35.50: 838 35.50 - 53.25: 176 53.25 - 71.00: 74 71.00 - 88.75: 17 Dihedral angle restraints: 7250 sinusoidal: 3217 harmonic: 4033 Sorted by residual: dihedral pdb=" C4' U G 12 " pdb=" C3' U G 12 " pdb=" C2' U G 12 " pdb=" C1' U G 12 " ideal model delta sinusoidal sigma weight residual 36.35 -39.06 75.41 1 3.10e+00 1.04e-01 7.47e+02 dihedral pdb=" C4' A G 14 " pdb=" C3' A G 14 " pdb=" C2' A G 14 " pdb=" C1' A G 14 " ideal model delta sinusoidal sigma weight residual 36.35 -37.00 73.34 1 3.10e+00 1.04e-01 7.13e+02 dihedral pdb=" C4' G G 23 " pdb=" C3' G G 23 " pdb=" C2' G G 23 " pdb=" C1' G G 23 " ideal model delta sinusoidal sigma weight residual 36.35 -36.24 72.59 1 3.10e+00 1.04e-01 7.00e+02 ... (remaining 7247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1473 0.098 - 0.196: 225 0.196 - 0.294: 44 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.840 Find NCS groups from input model: 0.050 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4562 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= 0.602 Angle : 1.128 10.494 16336 Z= 0.643 Chirality : 0.077 0.490 1747 Planarity : 0.007 0.066 1999 Dihedral : 17.686 88.755 4650 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/Z covalent geometry : bond 0.01333 / 0.60 (12068) covalent geometry : angle 1.12782 / 0.64 (16336) hydrogen bonds : bond 0.12095 / 7.73 ( 458) hydrogen bonds : angle 6.67492 / 4.60 ( 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: 0.1356 time to fit residues: 63.6518 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 : 0.502 ------------------------------------------------------------------------------- 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... 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 = 0.4423 r_free = 0.4423 target = 0.201291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.156638 restraints weight = 20118.458| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 3.46 r_work: 0.3808 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5460 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12068 Z= 0.154 Angle : 0.749 10.201 16336 Z= 0.371 Chirality : 0.049 0.287 1747 Planarity : 0.004 0.046 1999 Dihedral : 11.249 148.132 1793 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.84 % Allowed : 17.27 % Favored : 79.89 % 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: -2.94 (0.21), residues: 1346 helix: -1.04 (0.19), residues: 641 sheet: -2.84 (0.47), residues: 105 loop : -2.79 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 18 TYR 0.019 0.002 TYR A 403 PHE 0.034 0.002 PHE A 931 TRP 0.005 0.001 TRP A1193 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (12068) covalent geometry : angle 0.74900 / 0.37 (16336) hydrogen bonds : bond 0.03755 / 2.45 ( 458) hydrogen bonds : angle 5.04776 / 3.52 ( 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 268 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.445 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: A 102 ARG cc_start: 0.5835 (ptp-170) cc_final: 0.5511 (ptp-110) REVERT: A 119 PHE cc_start: 0.4796 (m-80) cc_final: 0.4349 (m-80) REVERT: A 120 LYS cc_start: 0.7446 (mmmt) cc_final: 0.6802 (ptpp) REVERT: A 152 THR cc_start: 0.6080 (t) cc_final: 0.5858 (m) REVERT: A 162 PHE cc_start: 0.7452 (m-80) cc_final: 0.7201 (m-80) REVERT: A 230 THR cc_start: 0.5266 (t) cc_final: 0.4844 (p) REVERT: A 272 LYS cc_start: 0.6363 (mttp) cc_final: 0.5986 (ttmm) REVERT: A 412 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6792 (tp30) REVERT: A 494 TYR cc_start: 0.5453 (t80) cc_final: 0.5202 (t80) REVERT: A 559 ASP cc_start: 0.7145 (m-30) cc_final: 0.5788 (m-30) REVERT: A 597 PHE cc_start: 0.4308 (m-10) cc_final: 0.3923 (m-80) REVERT: A 646 TYR cc_start: 0.6078 (t80) cc_final: 0.5862 (t80) REVERT: A 735 GLN cc_start: 0.5956 (OUTLIER) cc_final: 0.5656 (mp-120) REVERT: A 782 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.7758 (p0) REVERT: B 3 LYS cc_start: 0.6599 (tppt) cc_final: 0.5986 (tptp) REVERT: B 15 LYS cc_start: 0.8314 (tppt) cc_final: 0.8015 (tppt) REVERT: B 100 TRP cc_start: 0.6126 (OUTLIER) cc_final: 0.5663 (p90) REVERT: B 155 ARG cc_start: 0.5985 (mmm-85) cc_final: 0.4910 (tpp80) outliers start: 35 outliers final: 14 residues processed: 257 average time/residue: 0.1103 time to fit residues: 40.7453 Evaluate side-chains 188 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 400 LEU 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 782 ASP 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: 4.9990 chunk 41 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 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** A1139 ASN ** B 67 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 = 0.4195 r_free = 0.4195 target = 0.177440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131782 restraints weight = 19767.192| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.33 r_work: 0.3539 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 1.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 12068 Z= 0.308 Angle : 0.982 15.026 16336 Z= 0.499 Chirality : 0.061 0.548 1747 Planarity : 0.006 0.075 1999 Dihedral : 11.425 143.096 1784 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 5.19 % Allowed : 18.41 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.14 (0.20), residues: 1346 helix: -1.08 (0.19), residues: 637 sheet: -3.51 (0.41), residues: 111 loop : -2.90 (0.22), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 788 TYR 0.029 0.003 TYR A 995 PHE 0.022 0.003 PHE A1127 TRP 0.023 0.003 TRP A 355 HIS 0.008 0.002 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.31 (12068) covalent geometry : angle 0.98223 / 0.50 (16336) hydrogen bonds : bond 0.05545 / 3.68 ( 458) hydrogen bonds : angle 5.69982 / 4.02 ( 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 334 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 270 time to evaluate : 0.370 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: A 102 ARG cc_start: 0.7016 (ptp-170) cc_final: 0.6739 (ptp-170) REVERT: A 119 PHE cc_start: 0.6209 (m-80) cc_final: 0.5498 (m-80) REVERT: A 120 LYS cc_start: 0.7985 (mmmt) cc_final: 0.7305 (ptpp) REVERT: A 152 THR cc_start: 0.6728 (t) cc_final: 0.6324 (m) REVERT: A 159 GLU cc_start: 0.6916 (tm-30) cc_final: 0.6683 (tm-30) REVERT: A 224 PHE cc_start: 0.7691 (m-80) cc_final: 0.7152 (m-80) REVERT: A 238 ASN cc_start: 0.7693 (m-40) cc_final: 0.7183 (m110) REVERT: A 412 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7442 (tp30) REVERT: A 423 ASP cc_start: 0.8495 (p0) cc_final: 0.8240 (p0) REVERT: A 448 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8535 (mppt) REVERT: A 466 PHE cc_start: 0.8331 (t80) cc_final: 0.7743 (t80) REVERT: A 467 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7725 (tm-30) REVERT: A 471 LYS cc_start: 0.7611 (tppt) cc_final: 0.7228 (mtpp) REVERT: A 494 TYR cc_start: 0.6714 (t80) cc_final: 0.6461 (t80) REVERT: A 584 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7957 (mttt) REVERT: A 645 ARG cc_start: 0.8025 (mtp180) cc_final: 0.7738 (ttm-80) REVERT: A 654 ASP cc_start: 0.8346 (t0) cc_final: 0.8081 (t0) REVERT: A 692 LYS cc_start: 0.8368 (ttpp) cc_final: 0.7892 (tptt) REVERT: A 693 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7670 (tt) REVERT: A 708 ASP cc_start: 0.8596 (t70) cc_final: 0.8294 (t70) REVERT: A 728 PHE cc_start: 0.8345 (m-80) cc_final: 0.8137 (m-80) REVERT: A 858 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7597 (mm-30) REVERT: A 867 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8215 (mtp85) REVERT: A 883 ARG cc_start: 0.6212 (ttp-170) cc_final: 0.5272 (ttp80) REVERT: A 894 GLU cc_start: 0.8144 (tp30) cc_final: 0.7919 (tp30) REVERT: A 945 LYS cc_start: 0.7736 (ttmt) cc_final: 0.7389 (tttm) REVERT: A 999 TRP cc_start: 0.7593 (m-10) cc_final: 0.7183 (m-10) REVERT: A 1138 ARG cc_start: 0.7526 (ttt90) cc_final: 0.7071 (ttp80) REVERT: A 1149 PHE cc_start: 0.6602 (p90) cc_final: 0.6258 (p90) REVERT: A 1163 ASP cc_start: 0.7480 (m-30) cc_final: 0.6815 (t0) REVERT: A 1211 ILE cc_start: 0.5411 (OUTLIER) cc_final: 0.4807 (mp) REVERT: A 1217 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: B 15 LYS cc_start: 0.8435 (tppt) cc_final: 0.8136 (tppt) REVERT: B 29 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5236 (pm20) REVERT: B 56 SER cc_start: 0.8029 (OUTLIER) cc_final: 0.7726 (p) REVERT: B 100 TRP cc_start: 0.7604 (OUTLIER) cc_final: 0.6526 (p90) REVERT: B 121 ASP cc_start: 0.6653 (t70) cc_final: 0.6135 (p0) REVERT: B 129 GLU cc_start: 0.7515 (pt0) cc_final: 0.6962 (mp0) REVERT: B 155 ARG cc_start: 0.7134 (mmm-85) cc_final: 0.6918 (ttp-170) REVERT: B 156 ARG cc_start: 0.6726 (tmm-80) cc_final: 0.6371 (ttt180) outliers start: 64 outliers final: 22 residues processed: 319 average time/residue: 0.1194 time to fit residues: 53.0726 Evaluate side-chains 214 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 245 VAL 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 469 TYR Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 534 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 777 THR 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 1182 ASN Chi-restraints excluded: chain A residue 1211 ILE 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: 3.9990 chunk 86 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN A 735 GLN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4125 r_free = 0.4125 target = 0.171088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126651 restraints weight = 19103.190| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.24 r_work: 0.3472 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 1.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12068 Z= 0.170 Angle : 0.740 9.159 16336 Z= 0.372 Chirality : 0.051 0.452 1747 Planarity : 0.004 0.042 1999 Dihedral : 10.362 145.597 1781 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.97 % Allowed : 22.47 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.22), residues: 1346 helix: -0.41 (0.21), residues: 640 sheet: -2.95 (0.41), residues: 117 loop : -2.75 (0.23), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 543 TYR 0.028 0.002 TYR A 616 PHE 0.030 0.002 PHE A1198 TRP 0.008 0.001 TRP A1193 HIS 0.006 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (12068) covalent geometry : angle 0.74028 / 0.37 (16336) hydrogen bonds : bond 0.03860 / 2.50 ( 458) hydrogen bonds : angle 4.92325 / 3.44 ( 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 277 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7006 (ptp-170) cc_final: 0.6723 (ptp-170) REVERT: A 120 LYS cc_start: 0.7864 (mmmt) cc_final: 0.7285 (ptpp) REVERT: A 159 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6726 (tm-30) REVERT: A 178 GLU cc_start: 0.8126 (tp30) cc_final: 0.7907 (tp30) REVERT: A 187 MET cc_start: 0.3485 (tpp) cc_final: 0.3149 (tpp) REVERT: A 224 PHE cc_start: 0.7563 (m-80) cc_final: 0.7025 (m-80) REVERT: A 257 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8232 (pt0) REVERT: A 399 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 448 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8699 (mppt) REVERT: A 466 PHE cc_start: 0.8497 (t80) cc_final: 0.7901 (t80) REVERT: A 467 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 471 LYS cc_start: 0.7747 (tppt) cc_final: 0.7361 (mtpp) REVERT: A 539 GLU cc_start: 0.7284 (pm20) cc_final: 0.7052 (tt0) REVERT: A 562 TYR cc_start: 0.8048 (m-80) cc_final: 0.7733 (m-80) REVERT: A 565 CYS cc_start: 0.7934 (m) cc_final: 0.7711 (m) REVERT: A 603 MET cc_start: 0.7568 (mtp) cc_final: 0.7218 (mtm) REVERT: A 626 MET cc_start: 0.5696 (mmp) cc_final: 0.5426 (mmt) REVERT: A 645 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7691 (ttm-80) REVERT: A 653 TYR cc_start: 0.6472 (m-10) cc_final: 0.6000 (m-10) REVERT: A 708 ASP cc_start: 0.8680 (t70) cc_final: 0.8361 (t70) REVERT: A 811 LYS cc_start: 0.7914 (ttmm) cc_final: 0.7637 (tttm) REVERT: A 822 HIS cc_start: 0.7766 (m-70) cc_final: 0.7556 (m-70) REVERT: A 852 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: A 858 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7254 (mm-30) REVERT: A 867 ARG cc_start: 0.8426 (ptp-110) cc_final: 0.8151 (mtp85) REVERT: A 894 GLU cc_start: 0.8148 (tp30) cc_final: 0.7877 (pp20) REVERT: A 914 LEU cc_start: 0.8385 (tp) cc_final: 0.8140 (mm) REVERT: A 1104 ILE cc_start: 0.7518 (mm) cc_final: 0.6940 (tp) REVERT: A 1163 ASP cc_start: 0.7579 (m-30) cc_final: 0.7214 (t0) REVERT: A 1211 ILE cc_start: 0.6067 (OUTLIER) cc_final: 0.5629 (mt) REVERT: B 16 LYS cc_start: 0.5633 (OUTLIER) cc_final: 0.5261 (mtpp) REVERT: B 29 GLU cc_start: 0.5638 (OUTLIER) cc_final: 0.4965 (pm20) REVERT: B 76 GLU cc_start: 0.8290 (tp30) cc_final: 0.8087 (tm-30) REVERT: B 92 ILE cc_start: 0.8650 (mp) cc_final: 0.7853 (mt) REVERT: B 94 ASP cc_start: 0.8371 (p0) cc_final: 0.7954 (p0) REVERT: B 100 TRP cc_start: 0.7593 (OUTLIER) cc_final: 0.6571 (p90) REVERT: B 121 ASP cc_start: 0.6845 (t70) cc_final: 0.6295 (p0) REVERT: B 129 GLU cc_start: 0.7877 (pt0) cc_final: 0.7197 (mp0) REVERT: B 156 ARG cc_start: 0.6649 (tmm-80) cc_final: 0.6304 (ttt180) outliers start: 49 outliers final: 26 residues processed: 268 average time/residue: 0.1217 time to fit residues: 45.9358 Evaluate side-chains 213 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU 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 357 VAL Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 469 TYR 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 757 VAL Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 852 GLU Chi-restraints excluded: chain A residue 992 PHE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1130 LEU 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 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 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: 0.9990 chunk 124 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 116 optimal weight: 0.9990 chunk 82 optimal weight: 0.1980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN A 735 GLN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 ASN A1186 ASN A1197 GLN B 67 GLN B 89 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.172277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125027 restraints weight = 18996.607| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.27 r_work: 0.3471 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 1.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12068 Z= 0.129 Angle : 0.691 11.301 16336 Z= 0.345 Chirality : 0.049 0.358 1747 Planarity : 0.004 0.039 1999 Dihedral : 10.099 145.407 1781 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.41 % Allowed : 23.52 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.22), residues: 1346 helix: -0.08 (0.21), residues: 647 sheet: -2.66 (0.43), residues: 119 loop : -2.52 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 737 TYR 0.022 0.001 TYR A 616 PHE 0.038 0.001 PHE A1198 TRP 0.021 0.001 TRP A1193 HIS 0.007 0.001 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (12068) covalent geometry : angle 0.69128 / 0.34 (16336) hydrogen bonds : bond 0.03332 / 2.18 ( 458) hydrogen bonds : angle 4.75461 / 3.32 ( 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 256 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7369 (ptpp) REVERT: A 123 ILE cc_start: 0.6826 (mm) cc_final: 0.6405 (mm) REVERT: A 159 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6657 (tt0) REVERT: A 178 GLU cc_start: 0.7966 (tp30) cc_final: 0.7637 (tp30) REVERT: A 181 THR cc_start: 0.7211 (t) cc_final: 0.6946 (t) REVERT: A 224 PHE cc_start: 0.7381 (m-80) cc_final: 0.6813 (m-80) REVERT: A 257 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8231 (pt0) REVERT: A 325 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5200 (t80) REVERT: A 399 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 423 ASP cc_start: 0.8534 (p0) cc_final: 0.8272 (p0) REVERT: A 466 PHE cc_start: 0.8525 (t80) cc_final: 0.7924 (t80) REVERT: A 467 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 539 GLU cc_start: 0.7434 (pm20) cc_final: 0.7107 (tt0) REVERT: A 621 PHE cc_start: 0.6176 (p90) cc_final: 0.5873 (p90) REVERT: A 701 MET cc_start: 0.8155 (tpp) cc_final: 0.7855 (ttt) REVERT: A 708 ASP cc_start: 0.8646 (t70) cc_final: 0.8362 (t70) REVERT: A 811 LYS cc_start: 0.8010 (ttmm) cc_final: 0.7760 (tttm) REVERT: A 815 GLU cc_start: 0.8686 (tp30) cc_final: 0.8389 (tp30) REVERT: A 836 ARG cc_start: 0.8156 (tpp-160) cc_final: 0.7768 (mpt180) REVERT: A 858 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7451 (mm-30) REVERT: A 867 ARG cc_start: 0.8431 (ptp-110) cc_final: 0.8124 (mtp85) REVERT: A 913 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7867 (tm-30) REVERT: A 914 LEU cc_start: 0.8424 (tp) cc_final: 0.8035 (mm) REVERT: A 949 MET cc_start: 0.8395 (tpp) cc_final: 0.8095 (mmt) REVERT: A 1104 ILE cc_start: 0.7057 (mm) cc_final: 0.6603 (tp) REVERT: A 1128 MET cc_start: 0.5784 (ttm) cc_final: 0.5509 (ppp) REVERT: A 1163 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7093 (t0) REVERT: A 1217 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7658 (mt-10) REVERT: B 15 LYS cc_start: 0.8413 (tppt) cc_final: 0.8104 (tppt) REVERT: B 29 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.4814 (pm20) REVERT: B 76 GLU cc_start: 0.8416 (tp30) cc_final: 0.8120 (tm-30) REVERT: B 94 ASP cc_start: 0.8272 (p0) cc_final: 0.8056 (p0) REVERT: B 100 TRP cc_start: 0.7583 (OUTLIER) cc_final: 0.6309 (p90) REVERT: B 121 ASP cc_start: 0.6870 (t70) cc_final: 0.6353 (p0) REVERT: B 122 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6342 (mt) REVERT: B 156 ARG cc_start: 0.6660 (tmm-80) cc_final: 0.6367 (ttt180) outliers start: 42 outliers final: 20 residues processed: 247 average time/residue: 0.1184 time to fit residues: 41.1422 Evaluate side-chains 213 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LEU 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 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 509 ASN 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 992 PHE 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 1130 LEU Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1163 ASP Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 56 SER 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: 9.9990 chunk 78 optimal weight: 0.0170 chunk 127 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 119 optimal weight: 0.0060 chunk 70 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.1438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 509 ASN A 613 GLN A 735 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 ASN A1172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.171533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127152 restraints weight = 18830.854| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.42 r_work: 0.3452 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 1.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12068 Z= 0.130 Angle : 0.683 10.515 16336 Z= 0.338 Chirality : 0.048 0.379 1747 Planarity : 0.004 0.037 1999 Dihedral : 9.940 144.449 1779 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.24 % Allowed : 25.55 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.23), residues: 1346 helix: 0.11 (0.21), residues: 640 sheet: -2.58 (0.46), residues: 109 loop : -2.41 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 182 TYR 0.020 0.001 TYR A 616 PHE 0.020 0.001 PHE A 621 TRP 0.026 0.001 TRP A1193 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (12068) covalent geometry : angle 0.68288 / 0.34 (16336) hydrogen bonds : bond 0.03279 / 2.15 ( 458) hydrogen bonds : angle 4.70026 / 3.30 ( 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 243 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8692 (mmm-85) cc_final: 0.8150 (ttt90) REVERT: A 159 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7071 (tt0) REVERT: A 224 PHE cc_start: 0.7418 (m-80) cc_final: 0.6856 (m-80) REVERT: A 257 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8236 (pt0) REVERT: A 302 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: A 307 THR cc_start: 0.8541 (t) cc_final: 0.8154 (p) REVERT: A 308 LEU cc_start: 0.8602 (mp) cc_final: 0.8385 (mp) REVERT: A 325 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.5143 (t80) REVERT: A 350 ASP cc_start: 0.8406 (m-30) cc_final: 0.8109 (t0) REVERT: A 399 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7820 (tm-30) REVERT: A 423 ASP cc_start: 0.8531 (p0) cc_final: 0.8279 (p0) REVERT: A 467 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7916 (tm-30) REVERT: A 471 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7404 (mmmm) REVERT: A 494 TYR cc_start: 0.7462 (t80) cc_final: 0.6741 (t80) REVERT: A 539 GLU cc_start: 0.7390 (pm20) cc_final: 0.7090 (tt0) REVERT: A 541 ASP cc_start: 0.7335 (t70) cc_final: 0.6974 (t0) REVERT: A 562 TYR cc_start: 0.8144 (m-80) cc_final: 0.7873 (m-10) REVERT: A 621 PHE cc_start: 0.6189 (p90) cc_final: 0.5907 (p90) REVERT: A 701 MET cc_start: 0.8122 (tpp) cc_final: 0.7723 (ttt) REVERT: A 708 ASP cc_start: 0.8616 (t70) cc_final: 0.8342 (t70) REVERT: A 811 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7867 (tttp) REVERT: A 815 GLU cc_start: 0.8699 (tp30) cc_final: 0.8395 (tp30) REVERT: A 836 ARG cc_start: 0.8224 (tpp-160) cc_final: 0.7897 (tpp-160) REVERT: A 858 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7609 (mm-30) REVERT: A 867 ARG cc_start: 0.8373 (ptp-110) cc_final: 0.7997 (mtp85) REVERT: A 913 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 914 LEU cc_start: 0.8493 (tp) cc_final: 0.8023 (mm) REVERT: A 949 MET cc_start: 0.8481 (tpp) cc_final: 0.8152 (mmt) REVERT: A 1104 ILE cc_start: 0.7290 (mm) cc_final: 0.6803 (tp) REVERT: A 1128 MET cc_start: 0.6217 (ttm) cc_final: 0.5827 (ppp) REVERT: A 1217 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7718 (mt-10) REVERT: B 16 LYS cc_start: 0.5605 (OUTLIER) cc_final: 0.5172 (mtpp) REVERT: B 25 THR cc_start: 0.6002 (m) cc_final: 0.5663 (p) REVERT: B 94 ASP cc_start: 0.8264 (p0) cc_final: 0.8024 (p0) REVERT: B 100 TRP cc_start: 0.7590 (OUTLIER) cc_final: 0.6259 (p90) REVERT: B 106 TYR cc_start: 0.7492 (p90) cc_final: 0.7236 (t80) REVERT: B 121 ASP cc_start: 0.6984 (t70) cc_final: 0.6490 (p0) REVERT: B 155 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7427 (ttt180) REVERT: B 156 ARG cc_start: 0.6879 (tmm-80) cc_final: 0.6599 (ttt180) outliers start: 40 outliers final: 23 residues processed: 232 average time/residue: 0.1142 time to fit residues: 37.6123 Evaluate side-chains 212 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 115 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 302 GLU 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 468 ASN Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 509 ASN 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 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 850 ILE 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 1130 LEU Chi-restraints excluded: chain A residue 1167 TYR 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 155 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 99 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 32 optimal weight: 0.0970 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 613 GLN A 735 GLN ** A 975 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 = 0.4086 r_free = 0.4086 target = 0.168207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.123557 restraints weight = 18888.712| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.39 r_work: 0.3407 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 1.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12068 Z= 0.149 Angle : 0.699 9.117 16336 Z= 0.350 Chirality : 0.049 0.396 1747 Planarity : 0.004 0.039 1999 Dihedral : 9.951 143.535 1779 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.49 % Allowed : 25.14 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.23), residues: 1346 helix: 0.12 (0.21), residues: 645 sheet: -2.28 (0.50), residues: 107 loop : -2.32 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 182 TYR 0.030 0.002 TYR A 510 PHE 0.017 0.001 PHE A 530 TRP 0.033 0.002 TRP A1193 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (12068) covalent geometry : angle 0.69897 / 0.35 (16336) hydrogen bonds : bond 0.03457 / 2.29 ( 458) hydrogen bonds : angle 4.68457 / 3.29 ( 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 236 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.8243 (ttt90) REVERT: A 120 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7429 (ptmm) REVERT: A 187 MET cc_start: 0.4073 (tpt) cc_final: 0.3828 (mmt) REVERT: A 224 PHE cc_start: 0.7474 (m-80) cc_final: 0.7144 (m-80) REVERT: A 257 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8214 (pt0) REVERT: A 302 GLU cc_start: 0.8033 (mp0) cc_final: 0.7632 (tt0) REVERT: A 308 LEU cc_start: 0.8637 (mp) cc_final: 0.8391 (mp) REVERT: A 325 PHE cc_start: 0.6384 (OUTLIER) cc_final: 0.5357 (t80) REVERT: A 326 LYS cc_start: 0.7604 (tppt) cc_final: 0.7271 (tttt) REVERT: A 399 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7846 (tm-30) REVERT: A 414 LEU cc_start: 0.7917 (mt) cc_final: 0.7559 (mt) REVERT: A 423 ASP cc_start: 0.8537 (p0) cc_final: 0.7913 (m-30) REVERT: A 467 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 471 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7393 (mmmm) REVERT: A 494 TYR cc_start: 0.7655 (t80) cc_final: 0.6844 (t80) REVERT: A 513 GLN cc_start: 0.7898 (pt0) cc_final: 0.7641 (pt0) REVERT: A 539 GLU cc_start: 0.7406 (pm20) cc_final: 0.7053 (tt0) REVERT: A 561 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8215 (ttpp) REVERT: A 562 TYR cc_start: 0.8044 (m-80) cc_final: 0.7177 (m-80) REVERT: A 653 TYR cc_start: 0.6573 (m-10) cc_final: 0.6265 (m-10) REVERT: A 701 MET cc_start: 0.8111 (tpp) cc_final: 0.7751 (ttt) REVERT: A 836 ARG cc_start: 0.8263 (tpp-160) cc_final: 0.7869 (mpt180) REVERT: A 858 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7621 (mm-30) REVERT: A 913 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7873 (tm-30) REVERT: A 914 LEU cc_start: 0.8444 (tp) cc_final: 0.7994 (mm) REVERT: A 949 MET cc_start: 0.8511 (tpp) cc_final: 0.8210 (mmt) REVERT: A 957 MET cc_start: 0.8837 (tpt) cc_final: 0.8093 (tpt) REVERT: A 1104 ILE cc_start: 0.7524 (mm) cc_final: 0.7066 (tp) REVERT: A 1128 MET cc_start: 0.6513 (ttm) cc_final: 0.6052 (ppp) REVERT: A 1217 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 16 LYS cc_start: 0.5663 (OUTLIER) cc_final: 0.5218 (mtpp) REVERT: B 25 THR cc_start: 0.6103 (m) cc_final: 0.5878 (p) REVERT: B 94 ASP cc_start: 0.8431 (p0) cc_final: 0.8108 (p0) REVERT: B 100 TRP cc_start: 0.7773 (OUTLIER) cc_final: 0.6098 (p90) REVERT: B 106 TYR cc_start: 0.7565 (p90) cc_final: 0.7219 (t80) REVERT: B 121 ASP cc_start: 0.7317 (t70) cc_final: 0.6648 (p0) REVERT: B 122 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6901 (mt) REVERT: B 156 ARG cc_start: 0.6964 (tmm-80) cc_final: 0.6589 (ttt180) outliers start: 43 outliers final: 26 residues processed: 225 average time/residue: 0.1087 time to fit residues: 34.7508 Evaluate side-chains 203 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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 357 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 469 TYR 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 757 VAL Chi-restraints excluded: chain A residue 783 VAL 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 1053 SER Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1167 TYR 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 122 LEU 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: 2.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 71 optimal weight: 0.0670 chunk 87 optimal weight: 10.0000 chunk 117 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 overall best weight: 2.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 862 ASN ** A 975 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 = 0.4025 r_free = 0.4025 target = 0.161900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115590 restraints weight = 19124.209| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.22 r_work: 0.3315 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 1.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12068 Z= 0.189 Angle : 0.765 10.831 16336 Z= 0.383 Chirality : 0.051 0.420 1747 Planarity : 0.004 0.057 1999 Dihedral : 10.150 142.924 1779 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.57 % Allowed : 26.28 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.23), residues: 1346 helix: 0.10 (0.21), residues: 652 sheet: -2.22 (0.51), residues: 105 loop : -2.29 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 737 TYR 0.021 0.002 TYR A 616 PHE 0.022 0.002 PHE A 638 TRP 0.036 0.003 TRP A1193 HIS 0.005 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (12068) covalent geometry : angle 0.76488 / 0.38 (16336) hydrogen bonds : bond 0.03927 / 2.61 ( 458) hydrogen bonds : angle 4.78959 / 3.35 ( 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 251 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7613 (mmmt) cc_final: 0.7381 (ptmm) REVERT: A 224 PHE cc_start: 0.7439 (m-80) cc_final: 0.7171 (m-80) REVERT: A 238 ASN cc_start: 0.7776 (m-40) cc_final: 0.7179 (m110) REVERT: A 257 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8157 (pt0) REVERT: A 302 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7701 (tt0) REVERT: A 325 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.5934 (t80) REVERT: A 423 ASP cc_start: 0.8543 (p0) cc_final: 0.8297 (p0) REVERT: A 467 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 468 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8072 (m110) REVERT: A 471 LYS cc_start: 0.7919 (mtpt) cc_final: 0.7454 (mmmm) REVERT: A 561 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8117 (ttpp) REVERT: A 562 TYR cc_start: 0.8264 (m-80) cc_final: 0.7549 (m-80) REVERT: A 653 TYR cc_start: 0.6969 (m-10) cc_final: 0.6557 (m-10) REVERT: A 656 ASN cc_start: 0.8712 (m-40) cc_final: 0.8384 (t0) REVERT: A 670 TYR cc_start: 0.8602 (m-10) cc_final: 0.8327 (m-10) REVERT: A 701 MET cc_start: 0.8144 (tpp) cc_final: 0.7731 (ttt) REVERT: A 836 ARG cc_start: 0.8360 (tpp-160) cc_final: 0.8069 (tpp-160) REVERT: A 852 GLU cc_start: 0.8028 (tt0) cc_final: 0.7476 (pt0) REVERT: A 914 LEU cc_start: 0.8426 (tp) cc_final: 0.8152 (mm) REVERT: A 947 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8227 (tt0) REVERT: A 949 MET cc_start: 0.8599 (tpp) cc_final: 0.8252 (mmt) REVERT: A 1054 ARG cc_start: 0.7195 (mpt180) cc_final: 0.6481 (mmm-85) REVERT: A 1102 TYR cc_start: 0.6968 (m-80) cc_final: 0.6710 (m-10) REVERT: A 1104 ILE cc_start: 0.7754 (mm) cc_final: 0.7101 (tp) REVERT: B 16 LYS cc_start: 0.5587 (OUTLIER) cc_final: 0.5147 (mtpp) REVERT: B 19 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6776 (tt0) REVERT: B 94 ASP cc_start: 0.8358 (p0) cc_final: 0.7979 (p0) REVERT: B 100 TRP cc_start: 0.7820 (OUTLIER) cc_final: 0.5882 (p90) REVERT: B 121 ASP cc_start: 0.7564 (t70) cc_final: 0.6786 (p0) REVERT: B 122 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7415 (mt) REVERT: B 156 ARG cc_start: 0.7324 (tmm-80) cc_final: 0.6987 (ttt180) outliers start: 44 outliers final: 26 residues processed: 245 average time/residue: 0.1009 time to fit residues: 34.8493 Evaluate side-chains 218 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 89 LYS Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE 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 452 VAL Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 469 TYR 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 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 905 SER 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 1053 SER Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1167 TYR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 100 TRP Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 130 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 0.2980 chunk 66 optimal weight: 2.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 468 ASN A 822 HIS ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.158274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112303 restraints weight = 19235.722| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.16 r_work: 0.3269 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 1.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12068 Z= 0.221 Angle : 0.814 11.219 16336 Z= 0.409 Chirality : 0.054 0.424 1747 Planarity : 0.004 0.054 1999 Dihedral : 10.303 143.401 1779 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.49 % Allowed : 26.52 % Favored : 69.99 % 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: -1.75 (0.23), residues: 1346 helix: 0.00 (0.21), residues: 652 sheet: -2.21 (0.51), residues: 105 loop : -2.31 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 935 TYR 0.027 0.002 TYR A1068 PHE 0.029 0.002 PHE A 190 TRP 0.039 0.003 TRP A1193 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (12068) covalent geometry : angle 0.81439 / 0.41 (16336) hydrogen bonds : bond 0.04005 / 2.62 ( 458) hydrogen bonds : angle 4.97496 / 3.45 ( 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 241 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.9287 (mmmt) cc_final: 0.8638 (pttp) REVERT: A 238 ASN cc_start: 0.7917 (m-40) cc_final: 0.7293 (m110) REVERT: A 257 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8172 (pt0) REVERT: A 308 LEU cc_start: 0.8579 (mt) cc_final: 0.8020 (mp) REVERT: A 325 PHE cc_start: 0.7187 (OUTLIER) cc_final: 0.6592 (t80) REVERT: A 326 LYS cc_start: 0.7963 (tppt) cc_final: 0.7762 (tttt) REVERT: A 423 ASP cc_start: 0.8568 (p0) cc_final: 0.8334 (p0) REVERT: A 467 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 471 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7710 (mmmm) REVERT: A 562 TYR cc_start: 0.8339 (m-80) cc_final: 0.8043 (m-80) REVERT: A 656 ASN cc_start: 0.8771 (m-40) cc_final: 0.8434 (t0) REVERT: A 670 TYR cc_start: 0.8873 (m-10) cc_final: 0.8626 (m-80) REVERT: A 808 ASN cc_start: 0.7904 (m-40) cc_final: 0.7459 (m-40) REVERT: A 836 ARG cc_start: 0.8349 (tpp-160) cc_final: 0.8057 (tpp-160) REVERT: A 852 GLU cc_start: 0.8107 (tt0) cc_final: 0.7642 (pt0) REVERT: A 858 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7977 (mm-30) REVERT: A 914 LEU cc_start: 0.8410 (tp) cc_final: 0.8126 (mm) REVERT: A 947 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8264 (tt0) REVERT: A 957 MET cc_start: 0.8853 (tpt) cc_final: 0.8120 (tpt) REVERT: A 965 CYS cc_start: 0.8152 (t) cc_final: 0.7856 (p) REVERT: A 1054 ARG cc_start: 0.7616 (mpt180) cc_final: 0.6846 (mmm-85) REVERT: A 1102 TYR cc_start: 0.7143 (m-80) cc_final: 0.6848 (m-10) REVERT: A 1126 SER cc_start: 0.8950 (t) cc_final: 0.8514 (p) REVERT: A 1131 MET cc_start: 0.8093 (mmm) cc_final: 0.7626 (tpp) REVERT: B 16 LYS cc_start: 0.5536 (OUTLIER) cc_final: 0.5009 (mtpp) REVERT: B 19 GLU cc_start: 0.7275 (tm-30) cc_final: 0.7011 (tt0) REVERT: B 94 ASP cc_start: 0.8318 (p0) cc_final: 0.7924 (p0) REVERT: B 100 TRP cc_start: 0.7833 (OUTLIER) cc_final: 0.5598 (p90) REVERT: B 121 ASP cc_start: 0.7784 (t70) cc_final: 0.7071 (p0) outliers start: 43 outliers final: 33 residues processed: 231 average time/residue: 0.0984 time to fit residues: 32.7653 Evaluate side-chains 221 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 89 LYS Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 197 PHE 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 357 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 480 THR 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 757 VAL Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 952 ASP 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 1053 SER Chi-restraints excluded: chain A residue 1130 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 67 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.162799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117704 restraints weight = 19370.217| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.17 r_work: 0.3378 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 1.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12068 Z= 0.186 Angle : 0.789 10.937 16336 Z= 0.394 Chirality : 0.051 0.405 1747 Planarity : 0.004 0.043 1999 Dihedral : 10.252 144.869 1779 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.84 % Allowed : 27.58 % Favored : 69.59 % 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: -1.62 (0.23), residues: 1346 helix: 0.11 (0.21), residues: 652 sheet: -2.24 (0.49), residues: 112 loop : -2.23 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 182 TYR 0.022 0.002 TYR A1068 PHE 0.022 0.002 PHE A 638 TRP 0.039 0.003 TRP A1193 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (12068) covalent geometry : angle 0.78934 / 0.39 (16336) hydrogen bonds : bond 0.03723 / 2.46 ( 458) hydrogen bonds : angle 4.85322 / 3.38 ( 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 229 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.404 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: A 116 LYS cc_start: 0.9218 (mmmt) cc_final: 0.8655 (pttp) REVERT: A 161 MET cc_start: 0.6434 (mmp) cc_final: 0.6067 (mtp) REVERT: A 238 ASN cc_start: 0.7832 (m-40) cc_final: 0.7200 (m110) REVERT: A 257 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8190 (pt0) REVERT: A 307 THR cc_start: 0.8944 (t) cc_final: 0.8662 (p) REVERT: A 325 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.6462 (t80) REVERT: A 423 ASP cc_start: 0.8638 (p0) cc_final: 0.8122 (m-30) REVERT: A 467 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 562 TYR cc_start: 0.8291 (m-80) cc_final: 0.8023 (m-80) REVERT: A 628 ASN cc_start: 0.7405 (t0) cc_final: 0.7177 (t0) REVERT: A 653 TYR cc_start: 0.7180 (m-10) cc_final: 0.6763 (m-10) REVERT: A 656 ASN cc_start: 0.8680 (m-40) cc_final: 0.8476 (t0) REVERT: A 670 TYR cc_start: 0.8906 (m-10) cc_final: 0.8697 (m-80) REVERT: A 835 GLU cc_start: 0.7622 (pm20) cc_final: 0.7331 (pm20) REVERT: A 836 ARG cc_start: 0.8342 (tpp-160) cc_final: 0.8020 (tpp-160) REVERT: A 914 LEU cc_start: 0.8563 (tp) cc_final: 0.8298 (mm) REVERT: A 957 MET cc_start: 0.8799 (tpt) cc_final: 0.8061 (tpt) REVERT: A 1054 ARG cc_start: 0.7846 (mpt180) cc_final: 0.7076 (mmm-85) REVERT: A 1126 SER cc_start: 0.9027 (t) cc_final: 0.8666 (p) REVERT: A 1131 MET cc_start: 0.8077 (mmm) cc_final: 0.7741 (tpp) REVERT: B 16 LYS cc_start: 0.5736 (OUTLIER) cc_final: 0.5200 (mtpp) REVERT: B 94 ASP cc_start: 0.8157 (p0) cc_final: 0.7806 (p0) REVERT: B 121 ASP cc_start: 0.7781 (t70) cc_final: 0.7169 (p0) outliers start: 35 outliers final: 30 residues processed: 221 average time/residue: 0.1019 time to fit residues: 32.6357 Evaluate side-chains 218 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 38 VAL Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 197 PHE 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 357 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 480 THR 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 905 SER Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 952 ASP 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 1130 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 0.3980 chunk 135 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 468 ASN ** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.164054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118479 restraints weight = 19264.451| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.25 r_work: 0.3366 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 1.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12068 Z= 0.132 Angle : 0.734 12.214 16336 Z= 0.364 Chirality : 0.048 0.375 1747 Planarity : 0.003 0.043 1999 Dihedral : 10.068 145.995 1779 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.51 % Allowed : 27.74 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.23), residues: 1346 helix: 0.24 (0.21), residues: 655 sheet: -2.32 (0.45), residues: 129 loop : -2.16 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 182 TYR 0.023 0.002 TYR B 136 PHE 0.025 0.001 PHE A 244 TRP 0.038 0.002 TRP A1193 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (12068) covalent geometry : angle 0.73384 / 0.36 (16336) hydrogen bonds : bond 0.03221 / 2.08 ( 458) hydrogen bonds : angle 4.75440 / 3.31 ( 1308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2949.96 seconds wall clock time: 51 minutes 34.43 seconds (3094.43 seconds total)