Starting phenix.real_space_refine on Sat Sep 12 01:48:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nmc_0446/09_2026/6nmc_0446.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nmc_0446/09_2026/6nmc_0446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nmc_0446/09_2026/6nmc_0446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nmc_0446/09_2026/6nmc_0446.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6nmc_0446/09_2026/6nmc_0446.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nmc_0446/09_2026/6nmc_0446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nmc_0446/09_2026/6nmc_0446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nmc_0446/09_2026/6nmc_0446.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 39 5.16 5 C 8096 2.51 5 N 2098 2.21 5 O 2548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 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: 12808 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1202, 9931 Classifications: {'peptide': 1202} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 25, 'TRANS': 1172} 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: "C" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1029 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain breaks: 2 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.53, per 1000 atoms: 0.20 Number of scatterers: 12808 At special positions: 0 Unit cell: (132.184, 108.732, 105.534, 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 39 16.00 P 25 15.00 Mg 2 11.99 O 2548 8.00 N 2098 7.00 C 8096 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: 0.70 Conformation dependent library (CDL) restraints added in 407.7 milliseconds 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2838 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 13 sheets defined 53.0% alpha, 4.8% beta 4 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.19 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: 4.475A 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 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' 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: 3.856A 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 341 through 353 removed outlier: 4.155A pdb=" N SER A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 371 removed outlier: 4.142A 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: 3.800A 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: 3.711A 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: 4.351A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 952 removed outlier: 3.702A pdb=" N TYR A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) 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: 4.183A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) removed outlier: 3.587A 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: 3.529A 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: 4.591A 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: 3.670A pdb=" N ASP B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 4.288A pdb=" N ALA C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.528A pdb=" N GLU C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.741A pdb=" N THR C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 162 removed outlier: 3.815A pdb=" N LEU C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS C 161 " --> pdb=" O ILE C 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: 3.588A 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 736 through 738 removed outlier: 3.657A 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: 3.692A pdb=" N HIS A 759 " --> pdb=" O VAL A 783 " (cutoff:3.500A) removed outlier: 3.777A 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 832 removed outlier: 3.594A pdb=" N VAL A 842 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 7.054A 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: 6.536A 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: 7.631A pdb=" N ILE A 996 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.085A 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: 3.845A 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 1070 through 1073 removed outlier: 3.878A pdb=" N ARG A1071 " --> pdb=" O VAL A1089 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A1089 " --> pdb=" O ARG A1071 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1138 through 1140 506 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 4109 1.35 - 1.50: 4532 1.50 - 1.66: 4415 1.66 - 1.81: 24 1.81 - 1.96: 41 Bond restraints: 13121 Sorted by residual: 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 4.74e+01 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 4.73e+01 bond pdb=" CG MET A 531 " pdb=" SD MET A 531 " ideal model delta sigma weight residual 1.803 1.963 -0.160 2.50e-02 1.60e+03 4.11e+01 bond pdb=" SD MET A 603 " pdb=" CE MET A 603 " ideal model delta sigma weight residual 1.791 1.951 -0.160 2.50e-02 1.60e+03 4.08e+01 bond pdb=" CG MET A 626 " pdb=" SD MET A 626 " ideal model delta sigma weight residual 1.803 1.962 -0.159 2.50e-02 1.60e+03 4.04e+01 ... (remaining 13116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 16700 2.34 - 4.68: 917 4.68 - 7.01: 104 7.01 - 9.35: 28 9.35 - 11.69: 7 Bond angle restraints: 17756 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 113.16 105.09 8.07 1.24e+00 6.50e-01 4.23e+01 angle pdb=" C GLY A 477 " pdb=" N LYS A 478 " pdb=" CA LYS A 478 " ideal model delta sigma weight residual 121.70 133.39 -11.69 1.80e+00 3.09e-01 4.22e+01 angle pdb=" C PHE A 220 " pdb=" CA PHE A 220 " pdb=" CB PHE A 220 " ideal model delta sigma weight residual 109.29 119.29 -10.00 1.82e+00 3.02e-01 3.02e+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 2.55e+01 angle pdb=" CA TRP C 100 " pdb=" C TRP C 100 " pdb=" O TRP C 100 " ideal model delta sigma weight residual 121.10 115.60 5.50 1.10e+00 8.26e-01 2.50e+01 ... (remaining 17751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6709 17.92 - 35.84: 902 35.84 - 53.75: 172 53.75 - 71.67: 74 71.67 - 89.59: 13 Dihedral angle restraints: 7870 sinusoidal: 3472 harmonic: 4398 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 36.34 -39.09 75.44 1 3.10e+00 1.04e-01 7.48e+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 36.34 -38.30 74.65 1 3.10e+00 1.04e-01 7.34e+02 dihedral pdb=" C4' A G 4 " pdb=" C3' A G 4 " pdb=" C2' A G 4 " pdb=" C1' A G 4 " ideal model delta sinusoidal sigma weight residual 36.34 -37.48 73.82 1 3.10e+00 1.04e-01 7.21e+02 ... (remaining 7867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1561 0.098 - 0.196: 270 0.196 - 0.293: 48 0.293 - 0.391: 8 0.391 - 0.489: 2 Chirality restraints: 1889 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 5.98e+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 2.24 0.40 2.00e-01 2.50e+01 4.00e+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 2.26 0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 1886 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 102 " 0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ASN C 102 " -0.061 2.00e-02 2.50e+03 pdb=" O ASN C 102 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE C 103 " 0.021 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 6.55e-02 6.86e+00 pdb=" N PRO A 129 " 0.113 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 delta sigma weight rms_deltas residual plane pdb=" CA SER A 599 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C SER A 599 " -0.045 2.00e-02 2.50e+03 pdb=" O SER A 599 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS A 600 " 0.015 2.00e-02 2.50e+03 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 266 2.59 - 3.17: 11018 3.17 - 3.75: 20420 3.75 - 4.32: 26700 4.32 - 4.90: 42382 Nonbonded interactions: 100786 Sorted by model distance: nonbonded pdb="MG MG G 101 " pdb=" O HOH G 202 " model vdw 2.015 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 201 " model vdw 2.031 2.170 nonbonded pdb=" OP2 A G 19 " pdb="MG MG A1301 " model vdw 2.032 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH G 203 " model vdw 2.036 2.170 nonbonded pdb="MG MG G 101 " pdb=" O HOH A1401 " model vdw 2.045 2.170 ... (remaining 100781 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 group one per residue 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.014 0.172 13121 Z= 0.638 Angle : 1.186 11.689 17756 Z= 0.684 Chirality : 0.080 0.489 1889 Planarity : 0.007 0.065 2188 Dihedral : 17.179 89.589 5032 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.19 % Favored : 89.40 % Rotamer: Outliers : 2.45 % Allowed : 14.04 % Favored : 83.51 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % 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: -4.23 (0.17), residues: 1462 helix: -2.34 (0.15), residues: 695 sheet: -3.03 (0.45), residues: 112 loop : -3.24 (0.20), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 508 TYR 0.029 0.003 TYR A 237 PHE 0.033 0.004 PHE A1161 TRP 0.037 0.003 TRP C 100 HIS 0.008 0.002 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.01362 / 0.64 (13121) covalent geometry : angle 1.18608 / 0.68 (17756) hydrogen bonds : bond 0.12769 / 8.32 ( 516) hydrogen bonds : angle 6.64998 / 4.39 ( 1469) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 359 time to evaluate : 0.456 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.9173 (t80) cc_final: 0.8924 (t80) REVERT: A 142 ASN cc_start: 0.8986 (t0) cc_final: 0.8695 (t0) REVERT: A 173 PHE cc_start: 0.9203 (t80) cc_final: 0.8995 (t80) REVERT: A 200 HIS cc_start: 0.9264 (m-70) cc_final: 0.9020 (m-70) REVERT: A 231 GLN cc_start: 0.9530 (pt0) cc_final: 0.8739 (pp30) REVERT: A 256 ASN cc_start: 0.9400 (m-40) cc_final: 0.9064 (p0) REVERT: A 325 PHE cc_start: 0.8755 (m-80) cc_final: 0.8357 (m-80) REVERT: A 407 ASP cc_start: 0.8416 (m-30) cc_final: 0.8190 (t0) REVERT: A 420 GLN cc_start: 0.9315 (tt0) cc_final: 0.9091 (tm-30) REVERT: A 435 LEU cc_start: 0.9605 (tp) cc_final: 0.9219 (tt) REVERT: A 459 LEU cc_start: 0.9348 (mt) cc_final: 0.8923 (mm) REVERT: A 490 PHE cc_start: 0.8855 (t80) cc_final: 0.8499 (t80) REVERT: A 498 LEU cc_start: 0.9226 (mt) cc_final: 0.8527 (mt) REVERT: A 555 LEU cc_start: 0.9372 (tp) cc_final: 0.8910 (tt) REVERT: A 675 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8431 (tm-30) REVERT: A 914 LEU cc_start: 0.9523 (tp) cc_final: 0.9159 (mt) REVERT: A 1013 LEU cc_start: 0.9050 (mp) cc_final: 0.8850 (mm) REVERT: A 1035 MET cc_start: 0.8363 (ptm) cc_final: 0.7682 (ppp) REVERT: A 1049 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: A 1186 ASN cc_start: 0.8612 (m-40) cc_final: 0.8398 (m110) REVERT: A 1195 ILE cc_start: 0.9621 (mt) cc_final: 0.9393 (tp) REVERT: B 97 PHE cc_start: 0.8225 (m-10) cc_final: 0.7792 (m-10) REVERT: B 100 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.7696 (p90) REVERT: B 140 MET cc_start: 0.9227 (mmp) cc_final: 0.8907 (mmp) REVERT: B 148 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8125 (mm110) REVERT: B 152 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8616 (tptp) REVERT: C 105 ASN cc_start: 0.8370 (m-40) cc_final: 0.8104 (m-40) REVERT: C 108 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7930 (mm-30) outliers start: 33 outliers final: 9 residues processed: 385 average time/residue: 0.1357 time to fit residues: 71.4409 Evaluate side-chains 219 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 33 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN A 613 GLN A 718 ASN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN A 873 HIS ** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 ASN B 18 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 ASN ** 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 = 0.3525 r_free = 0.3525 target = 0.078043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.051760 restraints weight = 55106.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.053784 restraints weight = 28761.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055091 restraints weight = 19167.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.055912 restraints weight = 14837.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.056400 restraints weight = 12692.151| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13121 Z= 0.204 Angle : 0.803 13.676 17756 Z= 0.405 Chirality : 0.055 0.464 1889 Planarity : 0.004 0.053 2188 Dihedral : 10.799 152.442 1908 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.88 % Favored : 94.05 % Rotamer: Outliers : 0.15 % Allowed : 3.86 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.63 (0.20), residues: 1462 helix: -0.87 (0.18), residues: 718 sheet: -2.54 (0.53), residues: 85 loop : -2.63 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 883 TYR 0.030 0.002 TYR A 840 PHE 0.022 0.002 PHE A 61 TRP 0.040 0.003 TRP B 100 HIS 0.004 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (13121) covalent geometry : angle 0.80266 / 0.41 (17756) hydrogen bonds : bond 0.04093 / 2.60 ( 516) hydrogen bonds : angle 5.23538 / 3.49 ( 1469) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 267 time to evaluate : 0.512 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: 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 13 LEU cc_start: 0.9698 (tp) cc_final: 0.9456 (tt) REVERT: A 81 PHE cc_start: 0.9460 (t80) cc_final: 0.9249 (t80) REVERT: A 120 LYS cc_start: 0.9324 (mppt) cc_final: 0.9040 (mmtm) REVERT: A 161 MET cc_start: 0.9448 (mtm) cc_final: 0.9066 (mtp) REVERT: A 179 ASN cc_start: 0.9294 (m110) cc_final: 0.8981 (m110) REVERT: A 350 ASP cc_start: 0.9306 (t0) cc_final: 0.9072 (t0) REVERT: A 355 TRP cc_start: 0.7932 (m-90) cc_final: 0.7004 (m-10) REVERT: A 384 ASP cc_start: 0.9589 (t0) cc_final: 0.9265 (m-30) REVERT: A 386 ARG cc_start: 0.9136 (ttm110) cc_final: 0.8917 (mmm-85) REVERT: A 390 LYS cc_start: 0.9652 (mmpt) cc_final: 0.9268 (ptpp) REVERT: A 407 ASP cc_start: 0.8994 (m-30) cc_final: 0.8791 (t0) REVERT: A 420 GLN cc_start: 0.9604 (tt0) cc_final: 0.9403 (tm-30) REVERT: A 427 LYS cc_start: 0.9729 (tmtt) cc_final: 0.9498 (tptp) REVERT: A 490 PHE cc_start: 0.9337 (t80) cc_final: 0.8953 (t80) REVERT: A 497 LEU cc_start: 0.9818 (tp) cc_final: 0.9607 (tp) REVERT: A 498 LEU cc_start: 0.9265 (mt) cc_final: 0.8993 (mt) REVERT: A 531 MET cc_start: 0.8983 (mtm) cc_final: 0.8701 (mtm) REVERT: A 671 ARG cc_start: 0.9189 (ttm110) cc_final: 0.8854 (ttm110) REVERT: A 675 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8636 (tm-30) REVERT: A 795 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8462 (mt-10) REVERT: A 832 ASP cc_start: 0.8322 (t0) cc_final: 0.7994 (t0) REVERT: A 938 VAL cc_start: 0.4691 (OUTLIER) cc_final: 0.3464 (t) REVERT: A 939 GLU cc_start: 0.7388 (mp0) cc_final: 0.6917 (mp0) REVERT: A 971 LEU cc_start: 0.9442 (mt) cc_final: 0.9051 (mp) REVERT: A 986 MET cc_start: 0.8052 (ppp) cc_final: 0.7625 (ppp) REVERT: A 1035 MET cc_start: 0.8880 (ptm) cc_final: 0.7848 (ppp) REVERT: A 1128 MET cc_start: 0.9208 (mmp) cc_final: 0.9008 (mmm) REVERT: B 36 GLN cc_start: 0.9536 (pt0) cc_final: 0.9300 (pt0) REVERT: B 47 ASN cc_start: 0.8794 (p0) cc_final: 0.8460 (p0) REVERT: B 71 ASN cc_start: 0.9422 (m-40) cc_final: 0.8876 (m-40) REVERT: B 84 TRP cc_start: 0.9264 (m100) cc_final: 0.9035 (m100) REVERT: B 106 TYR cc_start: 0.8975 (t80) cc_final: 0.8752 (t80) REVERT: B 136 TYR cc_start: 0.9631 (t80) cc_final: 0.9270 (t80) REVERT: B 145 GLU cc_start: 0.9240 (tp30) cc_final: 0.8948 (tp30) REVERT: B 146 LEU cc_start: 0.9599 (mt) cc_final: 0.9261 (mt) REVERT: C 45 HIS cc_start: 0.9709 (p-80) cc_final: 0.9404 (p-80) REVERT: C 105 ASN cc_start: 0.8965 (m-40) cc_final: 0.8049 (p0) REVERT: C 109 LEU cc_start: 0.7890 (mt) cc_final: 0.7561 (mt) REVERT: C 125 ASP cc_start: 0.7781 (m-30) cc_final: 0.7385 (m-30) REVERT: C 132 TYR cc_start: 0.9424 (t80) cc_final: 0.9214 (t80) outliers start: 2 outliers final: 1 residues processed: 269 average time/residue: 0.1210 time to fit residues: 46.0140 Evaluate side-chains 205 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 22 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 104 optimal weight: 0.2980 chunk 100 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 117 optimal weight: 0.0070 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 40.0000 chunk 45 optimal weight: 7.9990 overall best weight: 3.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN A 718 ASN ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 944 GLN A1136 GLN A1139 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.077501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.051414 restraints weight = 55831.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.053402 restraints weight = 28937.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.054649 restraints weight = 19293.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.055287 restraints weight = 15034.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.055868 restraints weight = 13105.651| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13121 Z= 0.161 Angle : 0.684 10.895 17756 Z= 0.353 Chirality : 0.050 0.358 1889 Planarity : 0.004 0.059 2188 Dihedral : 10.218 145.259 1908 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 0.30 % Allowed : 4.01 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.82 (0.22), residues: 1462 helix: -0.12 (0.19), residues: 717 sheet: -2.52 (0.50), residues: 93 loop : -2.27 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1144 TYR 0.041 0.002 TYR C 106 PHE 0.030 0.002 PHE C 44 TRP 0.022 0.002 TRP A1086 HIS 0.003 0.001 HIS A 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (13121) covalent geometry : angle 0.68444 / 0.35 (17756) hydrogen bonds : bond 0.03591 / 2.28 ( 516) hydrogen bonds : angle 5.05968 / 3.39 ( 1469) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 249 time to evaluate : 0.500 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: 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 13 LEU cc_start: 0.9652 (tp) cc_final: 0.9434 (tt) REVERT: A 62 ILE cc_start: 0.9658 (mm) cc_final: 0.9378 (pt) REVERT: A 64 ASP cc_start: 0.9472 (t70) cc_final: 0.9213 (m-30) REVERT: A 71 LEU cc_start: 0.9071 (tp) cc_final: 0.8634 (tp) REVERT: A 81 PHE cc_start: 0.9394 (t80) cc_final: 0.9186 (t80) REVERT: A 162 PHE cc_start: 0.9011 (m-80) cc_final: 0.8498 (m-80) REVERT: A 179 ASN cc_start: 0.9277 (m110) cc_final: 0.9038 (m110) REVERT: A 200 HIS cc_start: 0.9704 (m-70) cc_final: 0.9498 (m-70) REVERT: A 256 ASN cc_start: 0.9560 (m-40) cc_final: 0.9052 (p0) REVERT: A 355 TRP cc_start: 0.8047 (m-90) cc_final: 0.7575 (m-10) REVERT: A 390 LYS cc_start: 0.9688 (mmpt) cc_final: 0.9305 (ptpp) REVERT: A 424 GLU cc_start: 0.9483 (tp30) cc_final: 0.9191 (tp30) REVERT: A 427 LYS cc_start: 0.9765 (tmtt) cc_final: 0.9516 (tptp) REVERT: A 490 PHE cc_start: 0.9268 (t80) cc_final: 0.9012 (t80) REVERT: A 497 LEU cc_start: 0.9807 (tp) cc_final: 0.9600 (tp) REVERT: A 498 LEU cc_start: 0.9416 (mt) cc_final: 0.9079 (mt) REVERT: A 531 MET cc_start: 0.8923 (mtm) cc_final: 0.8719 (mtm) REVERT: A 558 MET cc_start: 0.8930 (mpp) cc_final: 0.8414 (mpp) REVERT: A 675 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8468 (tp30) REVERT: A 832 ASP cc_start: 0.8371 (t0) cc_final: 0.8039 (t0) REVERT: A 939 GLU cc_start: 0.7567 (mp0) cc_final: 0.7331 (mp0) REVERT: A 971 LEU cc_start: 0.9425 (mt) cc_final: 0.8883 (tp) REVERT: A 986 MET cc_start: 0.8002 (ppp) cc_final: 0.7757 (ptm) REVERT: A 1035 MET cc_start: 0.8799 (ptm) cc_final: 0.8040 (ppp) REVERT: A 1128 MET cc_start: 0.9163 (mmp) cc_final: 0.8137 (tpp) REVERT: A 1135 LEU cc_start: 0.9574 (mm) cc_final: 0.9316 (mm) REVERT: B 36 GLN cc_start: 0.9535 (pt0) cc_final: 0.9319 (pt0) REVERT: B 71 ASN cc_start: 0.9416 (m-40) cc_final: 0.8762 (m110) REVERT: B 94 ASP cc_start: 0.9007 (p0) cc_final: 0.8806 (p0) REVERT: B 100 TRP cc_start: 0.8260 (OUTLIER) cc_final: 0.7644 (p90) REVERT: B 145 GLU cc_start: 0.9250 (tp30) cc_final: 0.8975 (tp30) REVERT: B 146 LEU cc_start: 0.9652 (mt) cc_final: 0.9284 (mt) REVERT: B 158 ASP cc_start: 0.8346 (t0) cc_final: 0.7965 (t0) REVERT: C 45 HIS cc_start: 0.9526 (p-80) cc_final: 0.9099 (p-80) REVERT: C 94 ASP cc_start: 0.8422 (p0) cc_final: 0.8073 (p0) REVERT: C 105 ASN cc_start: 0.9013 (m-40) cc_final: 0.8299 (p0) REVERT: C 109 LEU cc_start: 0.8399 (mt) cc_final: 0.8090 (mt) REVERT: C 143 TYR cc_start: 0.8143 (t80) cc_final: 0.7619 (t80) outliers start: 4 outliers final: 1 residues processed: 251 average time/residue: 0.1248 time to fit residues: 43.8716 Evaluate side-chains 206 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 36 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 30.0000 chunk 136 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 91 optimal weight: 0.0570 chunk 39 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 overall best weight: 4.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 GLN ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.076048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.049993 restraints weight = 56127.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.051944 restraints weight = 29144.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.053156 restraints weight = 19584.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053947 restraints weight = 15247.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.054379 restraints weight = 13073.476| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13121 Z= 0.188 Angle : 0.689 10.818 17756 Z= 0.354 Chirality : 0.050 0.361 1889 Planarity : 0.004 0.064 2188 Dihedral : 10.156 141.363 1908 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.48 (0.22), residues: 1462 helix: 0.20 (0.20), residues: 723 sheet: -2.35 (0.50), residues: 93 loop : -2.17 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 98 TYR 0.022 0.002 TYR C 106 PHE 0.026 0.002 PHE C 44 TRP 0.035 0.003 TRP A1218 HIS 0.011 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (13121) covalent geometry : angle 0.68870 / 0.35 (17756) hydrogen bonds : bond 0.03443 / 2.18 ( 516) hydrogen bonds : angle 5.04455 / 3.38 ( 1469) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.652 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.9624 (tp) cc_final: 0.9393 (tt) REVERT: A 62 ILE cc_start: 0.9666 (mm) cc_final: 0.9367 (pt) REVERT: A 64 ASP cc_start: 0.9479 (t70) cc_final: 0.9033 (m-30) REVERT: A 71 LEU cc_start: 0.9095 (tp) cc_final: 0.8657 (tp) REVERT: A 162 PHE cc_start: 0.9246 (m-80) cc_final: 0.8374 (m-80) REVERT: A 256 ASN cc_start: 0.9610 (m-40) cc_final: 0.9109 (p0) REVERT: A 355 TRP cc_start: 0.8438 (m-90) cc_final: 0.8206 (m-10) REVERT: A 384 ASP cc_start: 0.9384 (p0) cc_final: 0.9182 (p0) REVERT: A 386 ARG cc_start: 0.9264 (ttm110) cc_final: 0.8953 (mtm-85) REVERT: A 390 LYS cc_start: 0.9689 (mmpt) cc_final: 0.9323 (ptpt) REVERT: A 407 ASP cc_start: 0.8880 (t70) cc_final: 0.8611 (t70) REVERT: A 427 LYS cc_start: 0.9791 (tmtt) cc_final: 0.9533 (tptp) REVERT: A 487 TYR cc_start: 0.9006 (m-80) cc_final: 0.8543 (m-80) REVERT: A 490 PHE cc_start: 0.9359 (t80) cc_final: 0.9119 (t80) REVERT: A 498 LEU cc_start: 0.9484 (mt) cc_final: 0.9129 (mt) REVERT: A 531 MET cc_start: 0.8976 (mtm) cc_final: 0.8758 (mtm) REVERT: A 558 MET cc_start: 0.8997 (mpp) cc_final: 0.8531 (mpp) REVERT: A 707 LYS cc_start: 0.9288 (pttp) cc_final: 0.8979 (ptmm) REVERT: A 832 ASP cc_start: 0.8482 (t0) cc_final: 0.8077 (t0) REVERT: A 944 GLN cc_start: 0.9348 (pt0) cc_final: 0.8930 (pt0) REVERT: A 947 GLU cc_start: 0.8758 (tp30) cc_final: 0.8479 (tp30) REVERT: A 986 MET cc_start: 0.8108 (ppp) cc_final: 0.7850 (ptm) REVERT: A 1035 MET cc_start: 0.8838 (ptm) cc_final: 0.8048 (ppp) REVERT: A 1128 MET cc_start: 0.9173 (mmp) cc_final: 0.8158 (tpp) REVERT: A 1135 LEU cc_start: 0.9591 (mm) cc_final: 0.9350 (mm) REVERT: B 36 GLN cc_start: 0.9557 (pt0) cc_final: 0.9333 (pt0) REVERT: B 47 ASN cc_start: 0.8854 (p0) cc_final: 0.8644 (p0) REVERT: B 125 ASP cc_start: 0.9129 (p0) cc_final: 0.8596 (p0) REVERT: B 145 GLU cc_start: 0.9282 (tp30) cc_final: 0.8983 (tp30) REVERT: B 146 LEU cc_start: 0.9680 (mt) cc_final: 0.9344 (mt) REVERT: B 158 ASP cc_start: 0.8398 (t0) cc_final: 0.8101 (t0) REVERT: C 52 PHE cc_start: 0.8512 (t80) cc_final: 0.8182 (t80) REVERT: C 94 ASP cc_start: 0.8736 (p0) cc_final: 0.8464 (p0) REVERT: C 97 PHE cc_start: 0.9255 (p90) cc_final: 0.9050 (p90) REVERT: C 105 ASN cc_start: 0.9039 (m-40) cc_final: 0.8527 (p0) REVERT: C 109 LEU cc_start: 0.8882 (mt) cc_final: 0.8463 (mt) REVERT: C 143 TYR cc_start: 0.8445 (t80) cc_final: 0.8111 (t80) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1358 time to fit residues: 46.7614 Evaluate side-chains 190 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN B 45 HIS C 91 HIS ** C 147 ASN ** 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 = 0.3477 r_free = 0.3477 target = 0.075100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.048942 restraints weight = 54689.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.050821 restraints weight = 28836.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.052000 restraints weight = 19577.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.052702 restraints weight = 15360.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.053170 restraints weight = 13276.732| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13121 Z= 0.209 Angle : 0.705 10.948 17756 Z= 0.364 Chirality : 0.051 0.371 1889 Planarity : 0.004 0.049 2188 Dihedral : 10.198 139.933 1908 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.32 (0.22), residues: 1462 helix: 0.33 (0.20), residues: 717 sheet: -2.60 (0.46), residues: 99 loop : -2.00 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 482 TYR 0.027 0.002 TYR A 429 PHE 0.023 0.002 PHE A1161 TRP 0.024 0.002 TRP A1086 HIS 0.004 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 (13121) covalent geometry : angle 0.70538 / 0.36 (17756) hydrogen bonds : bond 0.03470 / 2.21 ( 516) hydrogen bonds : angle 5.27144 / 3.54 ( 1469) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.570 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LEU cc_start: 0.9611 (tp) cc_final: 0.9400 (tt) REVERT: A 71 LEU cc_start: 0.8948 (tp) cc_final: 0.8485 (tp) REVERT: A 161 MET cc_start: 0.9426 (mtm) cc_final: 0.9183 (mtp) REVERT: A 162 PHE cc_start: 0.9115 (m-80) cc_final: 0.8526 (m-80) REVERT: A 179 ASN cc_start: 0.9156 (m110) cc_final: 0.8862 (m110) REVERT: A 256 ASN cc_start: 0.9613 (m-40) cc_final: 0.9098 (p0) REVERT: A 355 TRP cc_start: 0.8608 (m-90) cc_final: 0.8322 (m-10) REVERT: A 386 ARG cc_start: 0.9271 (ttm110) cc_final: 0.8636 (mmt180) REVERT: A 390 LYS cc_start: 0.9688 (mmpt) cc_final: 0.9332 (ptpt) REVERT: A 407 ASP cc_start: 0.8873 (t70) cc_final: 0.8629 (t70) REVERT: A 427 LYS cc_start: 0.9842 (tmtt) cc_final: 0.9569 (tptp) REVERT: A 446 LEU cc_start: 0.9450 (mm) cc_final: 0.9135 (tp) REVERT: A 487 TYR cc_start: 0.8952 (m-80) cc_final: 0.8563 (m-80) REVERT: A 490 PHE cc_start: 0.9329 (t80) cc_final: 0.9113 (t80) REVERT: A 498 LEU cc_start: 0.9376 (mt) cc_final: 0.9064 (mt) REVERT: A 531 MET cc_start: 0.8973 (mtm) cc_final: 0.8675 (mtm) REVERT: A 558 MET cc_start: 0.9084 (mpp) cc_final: 0.8678 (mpp) REVERT: A 675 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8585 (tm-30) REVERT: A 707 LYS cc_start: 0.9303 (pttp) cc_final: 0.8982 (ptmm) REVERT: A 832 ASP cc_start: 0.8617 (t0) cc_final: 0.8122 (t0) REVERT: A 944 GLN cc_start: 0.9434 (pt0) cc_final: 0.9010 (pt0) REVERT: A 952 ASP cc_start: 0.9077 (m-30) cc_final: 0.8762 (m-30) REVERT: A 986 MET cc_start: 0.7962 (ppp) cc_final: 0.7408 (ptm) REVERT: A 1035 MET cc_start: 0.8825 (ptm) cc_final: 0.8052 (ppp) REVERT: A 1128 MET cc_start: 0.9154 (mmp) cc_final: 0.8186 (tpp) REVERT: A 1135 LEU cc_start: 0.9580 (mm) cc_final: 0.9362 (mm) REVERT: B 30 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: B 136 TYR cc_start: 0.9407 (t80) cc_final: 0.9120 (t80) REVERT: B 145 GLU cc_start: 0.9273 (tp30) cc_final: 0.8986 (tp30) REVERT: B 146 LEU cc_start: 0.9700 (mt) cc_final: 0.9386 (mt) REVERT: B 164 GLN cc_start: 0.9553 (mm-40) cc_final: 0.9306 (mp10) REVERT: C 45 HIS cc_start: 0.9685 (p-80) cc_final: 0.9397 (p-80) REVERT: C 52 PHE cc_start: 0.8569 (t80) cc_final: 0.8223 (t80) REVERT: C 86 PHE cc_start: 0.8023 (p90) cc_final: 0.7716 (p90) REVERT: C 94 ASP cc_start: 0.8696 (p0) cc_final: 0.8191 (p0) REVERT: C 97 PHE cc_start: 0.9303 (p90) cc_final: 0.9089 (p90) REVERT: C 103 PHE cc_start: 0.8339 (m-10) cc_final: 0.8047 (m-10) REVERT: C 105 ASN cc_start: 0.9084 (m-40) cc_final: 0.8492 (p0) REVERT: C 109 LEU cc_start: 0.9102 (mt) cc_final: 0.8454 (mt) REVERT: C 125 ASP cc_start: 0.8036 (m-30) cc_final: 0.7410 (m-30) REVERT: C 143 TYR cc_start: 0.8409 (t80) cc_final: 0.7999 (t80) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.1275 time to fit residues: 41.8292 Evaluate side-chains 190 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.0670 chunk 125 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 40.0000 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 HIS ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS B 47 ASN C 91 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.077943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.051714 restraints weight = 52916.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053727 restraints weight = 27920.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.054989 restraints weight = 18863.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.055780 restraints weight = 14729.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.056119 restraints weight = 12631.302| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13121 Z= 0.120 Angle : 0.643 9.178 17756 Z= 0.327 Chirality : 0.048 0.334 1889 Planarity : 0.003 0.039 2188 Dihedral : 10.022 140.973 1908 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.15 % Allowed : 1.63 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.20 (0.22), residues: 1462 helix: 0.36 (0.20), residues: 724 sheet: -1.99 (0.51), residues: 90 loop : -1.98 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1189 TYR 0.032 0.001 TYR A 494 PHE 0.016 0.001 PHE A 224 TRP 0.047 0.002 TRP A1218 HIS 0.003 0.001 HIS A 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (13121) covalent geometry : angle 0.64332 / 0.33 (17756) hydrogen bonds : bond 0.03196 / 2.03 ( 516) hydrogen bonds : angle 4.89300 / 3.30 ( 1469) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.497 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 62 ILE cc_start: 0.9620 (mm) cc_final: 0.9339 (pt) REVERT: A 71 LEU cc_start: 0.8988 (tp) cc_final: 0.8515 (tp) REVERT: A 162 PHE cc_start: 0.9315 (m-80) cc_final: 0.8607 (m-80) REVERT: A 179 ASN cc_start: 0.9208 (m110) cc_final: 0.8948 (m110) REVERT: A 256 ASN cc_start: 0.9632 (m-40) cc_final: 0.9173 (p0) REVERT: A 328 PHE cc_start: 0.9348 (t80) cc_final: 0.9120 (t80) REVERT: A 386 ARG cc_start: 0.9193 (ttm110) cc_final: 0.8812 (mmt-90) REVERT: A 387 LYS cc_start: 0.9472 (mmmm) cc_final: 0.9230 (ptpp) REVERT: A 390 LYS cc_start: 0.9677 (mmpt) cc_final: 0.9316 (ptpp) REVERT: A 407 ASP cc_start: 0.8967 (t70) cc_final: 0.8693 (t70) REVERT: A 427 LYS cc_start: 0.9827 (tmtt) cc_final: 0.9546 (tptp) REVERT: A 446 LEU cc_start: 0.9418 (mm) cc_final: 0.9123 (tp) REVERT: A 476 GLU cc_start: 0.9226 (pp20) cc_final: 0.8373 (pp20) REVERT: A 490 PHE cc_start: 0.9319 (t80) cc_final: 0.9066 (t80) REVERT: A 505 ASP cc_start: 0.9125 (m-30) cc_final: 0.8913 (m-30) REVERT: A 531 MET cc_start: 0.8855 (mtm) cc_final: 0.8559 (mtm) REVERT: A 535 ASP cc_start: 0.9228 (m-30) cc_final: 0.8817 (t70) REVERT: A 558 MET cc_start: 0.9101 (mpp) cc_final: 0.8549 (mpp) REVERT: A 675 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8552 (tm-30) REVERT: A 707 LYS cc_start: 0.9217 (pttp) cc_final: 0.8916 (ptmm) REVERT: A 832 ASP cc_start: 0.8474 (t0) cc_final: 0.8138 (t0) REVERT: A 944 GLN cc_start: 0.9397 (pt0) cc_final: 0.9008 (pt0) REVERT: A 952 ASP cc_start: 0.8947 (m-30) cc_final: 0.8663 (m-30) REVERT: A 986 MET cc_start: 0.7831 (ppp) cc_final: 0.7547 (ptm) REVERT: A 1035 MET cc_start: 0.8725 (ptm) cc_final: 0.7952 (ppp) REVERT: A 1128 MET cc_start: 0.9137 (mmp) cc_final: 0.8137 (tpp) REVERT: A 1135 LEU cc_start: 0.9490 (mm) cc_final: 0.9222 (mm) REVERT: A 1151 ILE cc_start: 0.8781 (mm) cc_final: 0.8492 (mm) REVERT: B 82 ILE cc_start: 0.8847 (mm) cc_final: 0.7828 (mm) REVERT: B 145 GLU cc_start: 0.9225 (tp30) cc_final: 0.8916 (tp30) REVERT: B 146 LEU cc_start: 0.9714 (mt) cc_final: 0.9400 (mt) REVERT: C 45 HIS cc_start: 0.9704 (p-80) cc_final: 0.9448 (p-80) REVERT: C 94 ASP cc_start: 0.8766 (p0) cc_final: 0.8275 (p0) REVERT: C 105 ASN cc_start: 0.9185 (m-40) cc_final: 0.8648 (m-40) REVERT: C 143 TYR cc_start: 0.8434 (t80) cc_final: 0.8085 (t80) outliers start: 2 outliers final: 0 residues processed: 246 average time/residue: 0.1322 time to fit residues: 46.2851 Evaluate side-chains 191 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 146 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 ASN ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 147 ASN ** 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 = 0.3470 r_free = 0.3470 target = 0.074969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.049180 restraints weight = 56078.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.051032 restraints weight = 29412.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.052191 restraints weight = 19843.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.052888 restraints weight = 15660.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.053362 restraints weight = 13578.548| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13121 Z= 0.204 Angle : 0.718 10.604 17756 Z= 0.366 Chirality : 0.051 0.353 1889 Planarity : 0.004 0.049 2188 Dihedral : 10.121 139.381 1908 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.16 (0.22), residues: 1462 helix: 0.48 (0.20), residues: 733 sheet: -2.16 (0.45), residues: 110 loop : -2.04 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 482 TYR 0.019 0.002 TYR C 106 PHE 0.020 0.002 PHE A1161 TRP 0.021 0.002 TRP A1086 HIS 0.011 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (13121) covalent geometry : angle 0.71821 / 0.37 (17756) hydrogen bonds : bond 0.03348 / 2.11 ( 516) hydrogen bonds : angle 5.12309 / 3.42 ( 1469) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.508 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.8923 (tp) cc_final: 0.8480 (tp) REVERT: A 178 GLU cc_start: 0.9133 (pm20) cc_final: 0.8593 (pm20) REVERT: A 179 ASN cc_start: 0.8994 (m110) cc_final: 0.7781 (m110) REVERT: A 256 ASN cc_start: 0.9630 (m-40) cc_final: 0.9152 (p0) REVERT: A 328 PHE cc_start: 0.9348 (t80) cc_final: 0.9098 (t80) REVERT: A 386 ARG cc_start: 0.9227 (ttm110) cc_final: 0.8823 (mmt-90) REVERT: A 390 LYS cc_start: 0.9684 (mmpt) cc_final: 0.9323 (ptpp) REVERT: A 407 ASP cc_start: 0.8948 (t70) cc_final: 0.8705 (t70) REVERT: A 427 LYS cc_start: 0.9829 (tmtt) cc_final: 0.9549 (tptp) REVERT: A 446 LEU cc_start: 0.9444 (mm) cc_final: 0.9152 (tp) REVERT: A 487 TYR cc_start: 0.8945 (m-80) cc_final: 0.8549 (m-80) REVERT: A 490 PHE cc_start: 0.9325 (t80) cc_final: 0.8962 (t80) REVERT: A 505 ASP cc_start: 0.9274 (m-30) cc_final: 0.9063 (m-30) REVERT: A 531 MET cc_start: 0.8959 (mtm) cc_final: 0.8645 (mtm) REVERT: A 707 LYS cc_start: 0.9233 (pttp) cc_final: 0.8976 (ptmm) REVERT: A 832 ASP cc_start: 0.8579 (t0) cc_final: 0.8166 (t0) REVERT: A 944 GLN cc_start: 0.9476 (pt0) cc_final: 0.9087 (pt0) REVERT: A 952 ASP cc_start: 0.8999 (m-30) cc_final: 0.8731 (m-30) REVERT: A 1035 MET cc_start: 0.8793 (ptm) cc_final: 0.8033 (ppp) REVERT: A 1128 MET cc_start: 0.9127 (mmp) cc_final: 0.8160 (tpp) REVERT: A 1131 MET cc_start: 0.9262 (mmp) cc_final: 0.9045 (mmp) REVERT: B 36 GLN cc_start: 0.9548 (pt0) cc_final: 0.9231 (pt0) REVERT: B 129 GLU cc_start: 0.9420 (pt0) cc_final: 0.9048 (pp20) REVERT: B 130 LEU cc_start: 0.9638 (mt) cc_final: 0.8869 (mt) REVERT: B 133 ASP cc_start: 0.9440 (p0) cc_final: 0.9203 (p0) REVERT: B 136 TYR cc_start: 0.9441 (t80) cc_final: 0.9161 (t80) REVERT: B 145 GLU cc_start: 0.9225 (tp30) cc_final: 0.8938 (tp30) REVERT: B 146 LEU cc_start: 0.9744 (mt) cc_final: 0.9430 (mt) REVERT: B 148 GLN cc_start: 0.9573 (mm110) cc_final: 0.9319 (mm-40) REVERT: B 152 LYS cc_start: 0.9226 (tptp) cc_final: 0.8998 (tptp) REVERT: B 158 ASP cc_start: 0.8621 (t0) cc_final: 0.8394 (t0) REVERT: C 45 HIS cc_start: 0.9742 (p-80) cc_final: 0.9413 (p-80) REVERT: C 94 ASP cc_start: 0.8815 (p0) cc_final: 0.8312 (p0) REVERT: C 105 ASN cc_start: 0.9118 (m-40) cc_final: 0.8595 (p0) REVERT: C 109 LEU cc_start: 0.9275 (mt) cc_final: 0.8468 (mt) REVERT: C 143 TYR cc_start: 0.8449 (t80) cc_final: 0.8096 (t80) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1340 time to fit residues: 41.9998 Evaluate side-chains 184 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 108 optimal weight: 0.1980 chunk 121 optimal weight: 8.9990 chunk 113 optimal weight: 0.4980 chunk 88 optimal weight: 5.9990 chunk 96 optimal weight: 0.0770 chunk 90 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 102 optimal weight: 0.1980 chunk 91 optimal weight: 8.9990 overall best weight: 0.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 GLN ** B 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.078481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.052753 restraints weight = 53844.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.054793 restraints weight = 28406.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.056029 restraints weight = 19072.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056884 restraints weight = 14863.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.057356 restraints weight = 12737.621| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13121 Z= 0.123 Angle : 0.685 9.391 17756 Z= 0.343 Chirality : 0.049 0.330 1889 Planarity : 0.003 0.038 2188 Dihedral : 9.987 144.025 1908 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.05 (0.22), residues: 1462 helix: 0.43 (0.19), residues: 730 sheet: -1.93 (0.51), residues: 90 loop : -1.83 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 788 TYR 0.036 0.001 TYR A 840 PHE 0.014 0.001 PHE A 931 TRP 0.015 0.002 TRP C 100 HIS 0.011 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13121) covalent geometry : angle 0.68527 / 0.34 (17756) hydrogen bonds : bond 0.03144 / 2.00 ( 516) hydrogen bonds : angle 4.89547 / 3.27 ( 1469) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.540 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: symmetry clash REVERT: A 71 LEU cc_start: 0.8842 (tp) cc_final: 0.8382 (tp) REVERT: A 179 ASN cc_start: 0.8956 (m110) cc_final: 0.8752 (m110) REVERT: A 187 MET cc_start: 0.9191 (mtp) cc_final: 0.8976 (mtp) REVERT: A 256 ASN cc_start: 0.9620 (m-40) cc_final: 0.9159 (p0) REVERT: A 313 GLU cc_start: 0.9209 (pm20) cc_final: 0.8957 (pm20) REVERT: A 328 PHE cc_start: 0.9324 (t80) cc_final: 0.9054 (t80) REVERT: A 407 ASP cc_start: 0.8933 (t70) cc_final: 0.8683 (t70) REVERT: A 427 LYS cc_start: 0.9828 (tmtt) cc_final: 0.9551 (tptp) REVERT: A 446 LEU cc_start: 0.9421 (mm) cc_final: 0.9139 (tp) REVERT: A 487 TYR cc_start: 0.8871 (m-80) cc_final: 0.8512 (m-80) REVERT: A 490 PHE cc_start: 0.9316 (t80) cc_final: 0.9098 (t80) REVERT: A 497 LEU cc_start: 0.9831 (tp) cc_final: 0.9624 (tt) REVERT: A 505 ASP cc_start: 0.9153 (m-30) cc_final: 0.8951 (m-30) REVERT: A 531 MET cc_start: 0.8761 (mtm) cc_final: 0.8459 (mtm) REVERT: A 703 GLN cc_start: 0.8821 (tt0) cc_final: 0.8339 (tm-30) REVERT: A 832 ASP cc_start: 0.8452 (t0) cc_final: 0.8116 (t0) REVERT: A 944 GLN cc_start: 0.9431 (pt0) cc_final: 0.9022 (pt0) REVERT: A 952 ASP cc_start: 0.8859 (m-30) cc_final: 0.8557 (m-30) REVERT: A 986 MET cc_start: 0.7401 (ppp) cc_final: 0.6605 (ptm) REVERT: A 1035 MET cc_start: 0.8715 (ptm) cc_final: 0.7941 (ppp) REVERT: A 1128 MET cc_start: 0.9082 (mmp) cc_final: 0.8218 (tpp) REVERT: A 1151 ILE cc_start: 0.8549 (mm) cc_final: 0.7989 (mm) REVERT: B 129 GLU cc_start: 0.9350 (pt0) cc_final: 0.9004 (pp20) REVERT: B 130 LEU cc_start: 0.9596 (mt) cc_final: 0.8848 (mt) REVERT: B 136 TYR cc_start: 0.9387 (t80) cc_final: 0.9098 (t80) REVERT: B 145 GLU cc_start: 0.9192 (tp30) cc_final: 0.8887 (tp30) REVERT: B 146 LEU cc_start: 0.9708 (mt) cc_final: 0.9233 (mt) REVERT: C 45 HIS cc_start: 0.9764 (p-80) cc_final: 0.9497 (p-80) REVERT: C 94 ASP cc_start: 0.8880 (p0) cc_final: 0.8397 (p0) REVERT: C 105 ASN cc_start: 0.9157 (m-40) cc_final: 0.8725 (p0) REVERT: C 109 LEU cc_start: 0.9048 (mt) cc_final: 0.8103 (mt) REVERT: C 133 ASP cc_start: 0.9396 (m-30) cc_final: 0.9191 (m-30) REVERT: C 143 TYR cc_start: 0.8449 (t80) cc_final: 0.8079 (t80) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.1263 time to fit residues: 42.5199 Evaluate side-chains 185 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 101 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 142 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 5 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 822 HIS ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.073895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.047248 restraints weight = 56284.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.049041 restraints weight = 30021.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.050136 restraints weight = 20569.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.050838 restraints weight = 16410.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.051235 restraints weight = 14271.866| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13121 Z= 0.272 Angle : 0.793 11.607 17756 Z= 0.405 Chirality : 0.054 0.394 1889 Planarity : 0.004 0.052 2188 Dihedral : 10.216 147.229 1908 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.14 (0.22), residues: 1462 helix: 0.42 (0.19), residues: 731 sheet: -2.42 (0.45), residues: 102 loop : -1.88 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 385 TYR 0.036 0.002 TYR A 840 PHE 0.024 0.002 PHE A1161 TRP 0.043 0.003 TRP B 84 HIS 0.006 0.002 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.27 (13121) covalent geometry : angle 0.79278 / 0.41 (17756) hydrogen bonds : bond 0.03590 / 2.28 ( 516) hydrogen bonds : angle 5.33160 / 3.54 ( 1469) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.516 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: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.9006 (tp) cc_final: 0.8565 (tp) REVERT: A 179 ASN cc_start: 0.8976 (m110) cc_final: 0.8758 (m110) REVERT: A 256 ASN cc_start: 0.9681 (m-40) cc_final: 0.9213 (p0) REVERT: A 313 GLU cc_start: 0.9317 (pm20) cc_final: 0.9052 (pm20) REVERT: A 328 PHE cc_start: 0.9351 (t80) cc_final: 0.9013 (t80) REVERT: A 387 LYS cc_start: 0.9225 (ptpp) cc_final: 0.9014 (ptpp) REVERT: A 407 ASP cc_start: 0.9007 (t70) cc_final: 0.8804 (t70) REVERT: A 427 LYS cc_start: 0.9834 (tmtt) cc_final: 0.9583 (tptp) REVERT: A 446 LEU cc_start: 0.9459 (mm) cc_final: 0.9160 (tp) REVERT: A 476 GLU cc_start: 0.9300 (pp20) cc_final: 0.8957 (pp20) REVERT: A 531 MET cc_start: 0.8990 (mtm) cc_final: 0.8668 (mtm) REVERT: A 707 LYS cc_start: 0.9140 (ptmm) cc_final: 0.8790 (ptpp) REVERT: A 832 ASP cc_start: 0.8736 (t0) cc_final: 0.8275 (t0) REVERT: A 1035 MET cc_start: 0.8859 (ptm) cc_final: 0.8117 (ppp) REVERT: A 1128 MET cc_start: 0.9103 (mmp) cc_final: 0.8188 (tpp) REVERT: B 20 ASN cc_start: 0.8939 (m110) cc_final: 0.8059 (m110) REVERT: B 36 GLN cc_start: 0.9545 (pt0) cc_final: 0.9233 (pt0) REVERT: B 73 LYS cc_start: 0.9516 (mtmm) cc_final: 0.9231 (ptpp) REVERT: B 129 GLU cc_start: 0.9406 (pt0) cc_final: 0.9043 (pp20) REVERT: B 130 LEU cc_start: 0.9656 (mt) cc_final: 0.8939 (mt) REVERT: B 133 ASP cc_start: 0.9512 (p0) cc_final: 0.9221 (p0) REVERT: B 136 TYR cc_start: 0.9476 (t80) cc_final: 0.9130 (t80) REVERT: B 145 GLU cc_start: 0.9243 (tp30) cc_final: 0.8936 (tp30) REVERT: B 146 LEU cc_start: 0.9689 (mt) cc_final: 0.9353 (mt) REVERT: B 148 GLN cc_start: 0.9570 (mm110) cc_final: 0.9334 (mm-40) REVERT: B 164 GLN cc_start: 0.9374 (mm-40) cc_final: 0.9076 (mm-40) REVERT: C 94 ASP cc_start: 0.8890 (p0) cc_final: 0.8425 (p0) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1254 time to fit residues: 39.8025 Evaluate side-chains 174 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 55 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 12 optimal weight: 0.0670 chunk 82 optimal weight: 6.9990 overall best weight: 2.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 HIS ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.076105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050081 restraints weight = 55483.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.052003 restraints weight = 28707.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.053247 restraints weight = 19278.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.054033 restraints weight = 15036.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.054491 restraints weight = 12893.811| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13121 Z= 0.156 Angle : 0.725 10.352 17756 Z= 0.365 Chirality : 0.051 0.337 1889 Planarity : 0.003 0.035 2188 Dihedral : 10.083 146.469 1908 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.22), residues: 1462 helix: 0.50 (0.19), residues: 726 sheet: -2.05 (0.50), residues: 90 loop : -1.71 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1189 TYR 0.046 0.002 TYR A 494 PHE 0.027 0.002 PHE C 44 TRP 0.033 0.002 TRP B 84 HIS 0.012 0.002 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (13121) covalent geometry : angle 0.72529 / 0.36 (17756) hydrogen bonds : bond 0.03371 / 2.16 ( 516) hydrogen bonds : angle 5.22494 / 3.50 ( 1469) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.544 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 71 LEU cc_start: 0.8939 (tp) cc_final: 0.8513 (tp) REVERT: A 138 ILE cc_start: 0.9283 (tp) cc_final: 0.8629 (tp) REVERT: A 167 LYS cc_start: 0.9291 (tmtt) cc_final: 0.9085 (ttpt) REVERT: A 179 ASN cc_start: 0.9215 (m110) cc_final: 0.8866 (m110) REVERT: A 256 ASN cc_start: 0.9656 (m-40) cc_final: 0.9210 (p0) REVERT: A 313 GLU cc_start: 0.9345 (pm20) cc_final: 0.9058 (pm20) REVERT: A 328 PHE cc_start: 0.9358 (t80) cc_final: 0.8903 (t80) REVERT: A 387 LYS cc_start: 0.9202 (ptpp) cc_final: 0.8988 (ptpp) REVERT: A 427 LYS cc_start: 0.9852 (tmtt) cc_final: 0.9600 (tptp) REVERT: A 446 LEU cc_start: 0.9455 (mm) cc_final: 0.9156 (tp) REVERT: A 476 GLU cc_start: 0.9175 (pp20) cc_final: 0.8897 (pp20) REVERT: A 490 PHE cc_start: 0.9366 (t80) cc_final: 0.9096 (t80) REVERT: A 505 ASP cc_start: 0.9299 (m-30) cc_final: 0.9094 (m-30) REVERT: A 531 MET cc_start: 0.8920 (mtm) cc_final: 0.8580 (mtm) REVERT: A 707 LYS cc_start: 0.9207 (ptmm) cc_final: 0.8871 (ptpp) REVERT: A 832 ASP cc_start: 0.8521 (t0) cc_final: 0.8109 (t0) REVERT: A 986 MET cc_start: 0.7299 (ppp) cc_final: 0.6415 (ptm) REVERT: A 1035 MET cc_start: 0.8827 (ptm) cc_final: 0.7966 (ppp) REVERT: A 1128 MET cc_start: 0.9094 (mmp) cc_final: 0.8473 (tpp) REVERT: B 12 TYR cc_start: 0.9012 (t80) cc_final: 0.8797 (t80) REVERT: B 66 MET cc_start: 0.4621 (mmm) cc_final: 0.3735 (mmm) REVERT: B 73 LYS cc_start: 0.9500 (mtmm) cc_final: 0.9154 (ptpp) REVERT: B 82 ILE cc_start: 0.8776 (mm) cc_final: 0.8490 (mm) REVERT: B 129 GLU cc_start: 0.9372 (pt0) cc_final: 0.9056 (pp20) REVERT: B 130 LEU cc_start: 0.9596 (mt) cc_final: 0.8871 (mt) REVERT: B 133 ASP cc_start: 0.9488 (p0) cc_final: 0.9281 (p0) REVERT: B 136 TYR cc_start: 0.9477 (t80) cc_final: 0.9111 (t80) REVERT: B 145 GLU cc_start: 0.9222 (tp30) cc_final: 0.8915 (tp30) REVERT: B 146 LEU cc_start: 0.9666 (mt) cc_final: 0.9340 (mt) REVERT: B 148 GLN cc_start: 0.9566 (mm110) cc_final: 0.9329 (mm-40) REVERT: B 164 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8871 (mm-40) REVERT: C 45 HIS cc_start: 0.9698 (p90) cc_final: 0.9335 (p-80) REVERT: C 94 ASP cc_start: 0.8919 (p0) cc_final: 0.8446 (p0) REVERT: C 105 ASN cc_start: 0.9347 (p0) cc_final: 0.8643 (p0) REVERT: C 109 LEU cc_start: 0.9248 (mt) cc_final: 0.8260 (mt) REVERT: C 130 LEU cc_start: 0.9401 (tt) cc_final: 0.9195 (mp) REVERT: C 143 TYR cc_start: 0.8262 (t80) cc_final: 0.7749 (t80) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1246 time to fit residues: 39.8600 Evaluate side-chains 185 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 123 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN A 238 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.075749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.053524 restraints weight = 55734.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.052360 restraints weight = 30588.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.052874 restraints weight = 23118.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.053133 restraints weight = 19529.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.053298 restraints weight = 18173.857| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.6986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13121 Z= 0.153 Angle : 0.721 10.029 17756 Z= 0.364 Chirality : 0.051 0.350 1889 Planarity : 0.003 0.035 2188 Dihedral : 10.039 144.730 1908 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.22), residues: 1462 helix: 0.55 (0.19), residues: 719 sheet: -2.03 (0.49), residues: 90 loop : -1.54 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1189 TYR 0.029 0.001 TYR A 494 PHE 0.020 0.001 PHE C 44 TRP 0.037 0.002 TRP B 84 HIS 0.011 0.001 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (13121) covalent geometry : angle 0.72149 / 0.36 (17756) hydrogen bonds : bond 0.03358 / 2.18 ( 516) hydrogen bonds : angle 5.18722 / 3.51 ( 1469) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2554.67 seconds wall clock time: 45 minutes 11.99 seconds (2711.99 seconds total)