Starting phenix.real_space_refine on Wed Feb 4 04:21:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qed_53055/02_2026/9qed_53055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qed_53055/02_2026/9qed_53055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qed_53055/02_2026/9qed_53055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qed_53055/02_2026/9qed_53055.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qed_53055/02_2026/9qed_53055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qed_53055/02_2026/9qed_53055.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 5610 2.51 5 N 1505 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8748 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 976 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "A" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5987 Classifications: {'peptide': 743} Link IDs: {'PTRANS': 34, 'TRANS': 708} Chain breaks: 4 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1568 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "D" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 217 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Time building chain proxies: 2.29, per 1000 atoms: 0.26 Number of scatterers: 8748 At special positions: 0 Unit cell: (85.68, 95.88, 126.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1594 8.00 N 1505 7.00 C 5610 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: 0.75 Conformation dependent library (CDL) restraints added in 347.6 milliseconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 58.0% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'C' and resid 34 through 45 removed outlier: 3.628A pdb=" N GLU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYS C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 62 removed outlier: 4.283A pdb=" N GLU C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 58 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 60 " --> pdb=" O TYR C 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 40 through 52 Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.683A pdb=" N TYR A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.985A pdb=" N ALA A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.520A pdb=" N VAL A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 205 removed outlier: 3.501A pdb=" N PHE A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.667A pdb=" N ILE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 279 through 301 Processing helix chain 'A' and resid 302 through 320 Processing helix chain 'A' and resid 329 through 344 removed outlier: 3.774A pdb=" N SER A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 398 removed outlier: 4.426A pdb=" N GLU A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 427 through 440 Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.722A pdb=" N VAL A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'A' and resid 565 through 573 Processing helix chain 'A' and resid 584 through 598 removed outlier: 3.722A pdb=" N ARG A 598 " --> pdb=" O TYR A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 641 Processing helix chain 'A' and resid 689 through 692 removed outlier: 3.832A pdb=" N ARG A 692 " --> pdb=" O ARG A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 694 through 702 Processing helix chain 'A' and resid 729 through 739 Processing helix chain 'A' and resid 739 through 752 removed outlier: 3.753A pdb=" N SER A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 795 Processing helix chain 'A' and resid 805 through 817 removed outlier: 3.548A pdb=" N GLU A 811 " --> pdb=" O HIS A 807 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 817 " --> pdb=" O PHE A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 832 removed outlier: 4.185A pdb=" N THR A 832 " --> pdb=" O LEU A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 855 removed outlier: 3.753A pdb=" N ASP A 850 " --> pdb=" O PRO A 846 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 851 " --> pdb=" O GLY A 847 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET A 855 " --> pdb=" O PHE A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 870 removed outlier: 4.107A pdb=" N HIS A 868 " --> pdb=" O ARG A 864 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 879 Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 891 through 902 Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.845A pdb=" N GLY B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 156 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.691A pdb=" N LYS B 183 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 219 through 223 removed outlier: 4.126A pdb=" N LEU B 222 " --> pdb=" O PRO B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 267 through 274 removed outlier: 3.834A pdb=" N LEU B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 290 removed outlier: 4.160A pdb=" N LYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 533 removed outlier: 3.826A pdb=" N GLU D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 536 No H-bonds generated for 'chain 'D' and resid 534 through 536' Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 547 through 551 Processing sheet with id=AA1, first strand: chain 'C' and resid 76 through 78 removed outlier: 4.096A pdb=" N VAL C 115 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ALA C 14 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N PHE C 114 " --> pdb=" O ALA C 14 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU C 16 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL C 116 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASP C 18 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL C 118 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS C 20 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS C 98 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 408 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL A 212 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE A 609 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE A 214 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY A 611 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 216 " --> pdb=" O GLY A 611 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 76 through 78 removed outlier: 4.096A pdb=" N VAL C 115 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ALA C 14 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N PHE C 114 " --> pdb=" O ALA C 14 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU C 16 " --> pdb=" O PHE C 114 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL C 116 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASP C 18 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL C 118 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS C 20 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 13 " --> pdb=" O CYS C 10 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 removed outlier: 6.293A pdb=" N VAL A 59 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA A 109 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL A 61 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 58 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LEU A 132 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU A 60 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 32 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N TRP A 193 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 34 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 705 through 709 removed outlier: 6.693A pdb=" N ILE A 684 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 709 " --> pdb=" O ILE A 684 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL A 686 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 723 through 728 removed outlier: 5.817A pdb=" N CYS A 723 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 758 " --> pdb=" O CYS A 723 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLU A 725 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLU A 760 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS A 727 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 122 removed outlier: 5.704A pdb=" N ILE B 101 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 102 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N CYS B 137 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU B 170 " --> pdb=" O CYS B 137 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU B 139 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N GLN B 172 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU B 141 " --> pdb=" O GLN B 172 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2850 1.34 - 1.46: 1676 1.46 - 1.58: 4349 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 8928 Sorted by residual: bond pdb=" CB GLU A 248 " pdb=" CG GLU A 248 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CB GLU C 39 " pdb=" CG GLU C 39 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.34e-01 bond pdb=" CB MET A 182 " pdb=" CG MET A 182 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.24e-01 bond pdb=" CB ASN B 110 " pdb=" CG ASN B 110 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.88e-01 bond pdb=" CB ASN A 738 " pdb=" CG ASN A 738 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.00e-01 ... (remaining 8923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 11862 1.66 - 3.31: 184 3.31 - 4.97: 22 4.97 - 6.63: 9 6.63 - 8.29: 4 Bond angle restraints: 12081 Sorted by residual: angle pdb=" C LEU A 15 " pdb=" CA LEU A 15 " pdb=" CB LEU A 15 " ideal model delta sigma weight residual 115.89 110.44 5.45 1.32e+00 5.74e-01 1.71e+01 angle pdb=" CA GLU A 248 " pdb=" CB GLU A 248 " pdb=" CG GLU A 248 " ideal model delta sigma weight residual 114.10 122.20 -8.10 2.00e+00 2.50e-01 1.64e+01 angle pdb=" N ASP B 174 " pdb=" CA ASP B 174 " pdb=" C ASP B 174 " ideal model delta sigma weight residual 114.56 111.29 3.27 1.27e+00 6.20e-01 6.64e+00 angle pdb=" CB LYS C 79 " pdb=" CG LYS C 79 " pdb=" CD LYS C 79 " ideal model delta sigma weight residual 111.30 116.97 -5.67 2.30e+00 1.89e-01 6.08e+00 angle pdb=" CA ASN A 738 " pdb=" CB ASN A 738 " pdb=" CG ASN A 738 " ideal model delta sigma weight residual 112.60 114.98 -2.38 1.00e+00 1.00e+00 5.67e+00 ... (remaining 12076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4561 17.60 - 35.19: 660 35.19 - 52.79: 186 52.79 - 70.39: 17 70.39 - 87.98: 18 Dihedral angle restraints: 5442 sinusoidal: 2242 harmonic: 3200 Sorted by residual: dihedral pdb=" CA THR A 165 " pdb=" C THR A 165 " pdb=" N ASP A 166 " pdb=" CA ASP A 166 " ideal model delta harmonic sigma weight residual 180.00 156.33 23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA TYR A 344 " pdb=" C TYR A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA PHE C 70 " pdb=" C PHE C 70 " pdb=" N THR C 71 " pdb=" CA THR C 71 " ideal model delta harmonic sigma weight residual 180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 895 0.031 - 0.063: 334 0.063 - 0.094: 90 0.094 - 0.126: 56 0.126 - 0.157: 3 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CB ILE A 873 " pdb=" CA ILE A 873 " pdb=" CG1 ILE A 873 " pdb=" CG2 ILE A 873 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA ILE A 684 " pdb=" N ILE A 684 " pdb=" C ILE A 684 " pdb=" CB ILE A 684 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE B 101 " pdb=" N ILE B 101 " pdb=" C ILE B 101 " pdb=" CB ILE B 101 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1375 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 220 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 847 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO A 848 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 848 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 848 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 719 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO A 720 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 720 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 720 " 0.016 5.00e-02 4.00e+02 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1207 2.75 - 3.29: 8494 3.29 - 3.82: 14168 3.82 - 4.36: 16459 4.36 - 4.90: 28679 Nonbonded interactions: 69007 Sorted by model distance: nonbonded pdb=" O CYS B 238 " pdb=" OG1 THR B 241 " model vdw 2.212 3.040 nonbonded pdb=" OE2 GLU A 760 " pdb=" OG1 THR A 809 " model vdw 2.229 3.040 nonbonded pdb=" N GLU A 712 " pdb=" OE1 GLU A 712 " model vdw 2.234 3.120 nonbonded pdb=" NE2 GLN B 107 " pdb=" OH TYR B 130 " model vdw 2.235 3.120 nonbonded pdb=" OG1 THR A 165 " pdb=" O ASP A 166 " model vdw 2.241 3.040 ... (remaining 69002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.450 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8928 Z= 0.152 Angle : 0.533 8.287 12081 Z= 0.267 Chirality : 0.039 0.157 1378 Planarity : 0.003 0.032 1537 Dihedral : 17.834 87.982 3358 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.10 % Allowed : 29.55 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.27), residues: 1072 helix: 1.31 (0.23), residues: 527 sheet: -0.81 (0.41), residues: 179 loop : -0.80 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 95 TYR 0.005 0.001 TYR C 88 PHE 0.011 0.001 PHE A 607 TRP 0.004 0.001 TRP D 540 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8928) covalent geometry : angle 0.53320 (12081) hydrogen bonds : bond 0.21071 ( 433) hydrogen bonds : angle 6.22225 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 248 GLU cc_start: 0.7956 (tp30) cc_final: 0.7683 (mm-30) outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 0.1015 time to fit residues: 13.2314 Evaluate side-chains 93 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 137 HIS A 197 HIS A 243 HIS A 268 HIS A 286 GLN A 419 GLN ** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 251 GLN B 280 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.090885 restraints weight = 14164.398| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.47 r_work: 0.2969 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8928 Z= 0.167 Angle : 0.556 7.588 12081 Z= 0.282 Chirality : 0.041 0.142 1378 Planarity : 0.004 0.040 1537 Dihedral : 4.519 58.543 1187 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.82 % Allowed : 26.96 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 1072 helix: 1.56 (0.23), residues: 537 sheet: -0.82 (0.41), residues: 179 loop : -0.82 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 167 TYR 0.013 0.001 TYR C 88 PHE 0.023 0.001 PHE B 286 TRP 0.008 0.001 TRP A 450 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8928) covalent geometry : angle 0.55606 (12081) hydrogen bonds : bond 0.04959 ( 433) hydrogen bonds : angle 4.59811 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.281 Fit side-chains REVERT: C 5 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8109 (mmtm) REVERT: C 100 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7924 (mtp180) REVERT: A 263 ASP cc_start: 0.7708 (m-30) cc_final: 0.7443 (m-30) REVERT: B 110 ASN cc_start: 0.8421 (t0) cc_final: 0.8204 (t0) REVERT: B 157 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8798 (mm) REVERT: B 277 LEU cc_start: 0.8852 (mm) cc_final: 0.8620 (mm) outliers start: 37 outliers final: 20 residues processed: 127 average time/residue: 0.0989 time to fit residues: 16.8550 Evaluate side-chains 115 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain D residue 530 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 104 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS ** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.089385 restraints weight = 14079.970| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.45 r_work: 0.2939 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8928 Z= 0.243 Angle : 0.604 8.405 12081 Z= 0.305 Chirality : 0.043 0.151 1378 Planarity : 0.004 0.042 1537 Dihedral : 4.739 59.001 1187 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.17 % Allowed : 25.52 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.27), residues: 1072 helix: 1.46 (0.23), residues: 538 sheet: -0.91 (0.40), residues: 179 loop : -0.88 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 167 TYR 0.012 0.001 TYR C 88 PHE 0.021 0.002 PHE B 286 TRP 0.006 0.001 TRP A 450 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00593 ( 8928) covalent geometry : angle 0.60433 (12081) hydrogen bonds : bond 0.05241 ( 433) hydrogen bonds : angle 4.41278 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 0.338 Fit side-chains REVERT: C 5 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8216 (mmtm) REVERT: C 70 PHE cc_start: 0.5943 (OUTLIER) cc_final: 0.4919 (t80) REVERT: C 100 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8053 (mtp180) REVERT: C 120 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7903 (mm-40) REVERT: A 82 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: A 157 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8661 (mttm) REVERT: A 263 ASP cc_start: 0.7876 (m-30) cc_final: 0.7626 (m-30) REVERT: A 399 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6156 (mt-10) REVERT: B 110 ASN cc_start: 0.8420 (t0) cc_final: 0.8116 (t0) REVERT: B 157 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8813 (mm) REVERT: B 184 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: B 277 LEU cc_start: 0.8943 (mm) cc_final: 0.8680 (mm) outliers start: 50 outliers final: 34 residues processed: 134 average time/residue: 0.1044 time to fit residues: 18.9954 Evaluate side-chains 129 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 87 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain D residue 530 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS ** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.090595 restraints weight = 14266.051| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.54 r_work: 0.2948 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8928 Z= 0.161 Angle : 0.539 7.410 12081 Z= 0.271 Chirality : 0.041 0.141 1378 Planarity : 0.004 0.043 1537 Dihedral : 4.618 59.204 1187 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.17 % Allowed : 25.72 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 1072 helix: 1.57 (0.23), residues: 541 sheet: -0.87 (0.40), residues: 179 loop : -0.83 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.010 0.001 TYR C 88 PHE 0.020 0.001 PHE B 286 TRP 0.008 0.001 TRP A 450 HIS 0.006 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8928) covalent geometry : angle 0.53879 (12081) hydrogen bonds : bond 0.04453 ( 433) hydrogen bonds : angle 4.27056 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 95 time to evaluate : 0.439 Fit side-chains REVERT: C 5 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8150 (mmtm) REVERT: C 70 PHE cc_start: 0.5836 (OUTLIER) cc_final: 0.4860 (t80) REVERT: C 100 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7899 (mtp180) REVERT: A 263 ASP cc_start: 0.7640 (m-30) cc_final: 0.7403 (m-30) REVERT: B 110 ASN cc_start: 0.8435 (t0) cc_final: 0.8150 (t0) REVERT: B 157 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8826 (mm) REVERT: B 184 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: B 290 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6877 (p-80) outliers start: 50 outliers final: 34 residues processed: 139 average time/residue: 0.0973 time to fit residues: 18.4623 Evaluate side-chains 130 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain D residue 530 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 3 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.091521 restraints weight = 14146.931| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.53 r_work: 0.2963 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8928 Z= 0.132 Angle : 0.518 7.178 12081 Z= 0.260 Chirality : 0.040 0.142 1378 Planarity : 0.004 0.043 1537 Dihedral : 4.513 57.165 1187 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.48 % Allowed : 25.10 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.27), residues: 1072 helix: 1.71 (0.23), residues: 541 sheet: -0.86 (0.40), residues: 179 loop : -0.70 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.009 0.001 TYR C 88 PHE 0.019 0.001 PHE B 286 TRP 0.008 0.001 TRP A 450 HIS 0.008 0.001 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8928) covalent geometry : angle 0.51788 (12081) hydrogen bonds : bond 0.04056 ( 433) hydrogen bonds : angle 4.17674 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 99 time to evaluate : 0.243 Fit side-chains REVERT: C 5 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8097 (mmtm) REVERT: C 70 PHE cc_start: 0.5842 (OUTLIER) cc_final: 0.4864 (t80) REVERT: C 100 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8001 (mtp180) REVERT: C 120 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8104 (mm-40) REVERT: B 110 ASN cc_start: 0.8397 (t0) cc_final: 0.8104 (t0) REVERT: B 157 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8839 (mm) REVERT: B 184 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: B 248 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8581 (t) REVERT: B 290 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.6919 (p-80) outliers start: 53 outliers final: 38 residues processed: 143 average time/residue: 0.0727 time to fit residues: 14.5736 Evaluate side-chains 135 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 90 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain D residue 530 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.091982 restraints weight = 14118.091| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.52 r_work: 0.2986 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8928 Z= 0.123 Angle : 0.506 6.988 12081 Z= 0.254 Chirality : 0.040 0.160 1378 Planarity : 0.003 0.044 1537 Dihedral : 4.432 55.500 1187 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.17 % Allowed : 25.21 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.27), residues: 1072 helix: 1.78 (0.23), residues: 541 sheet: -0.80 (0.40), residues: 179 loop : -0.66 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.008 0.001 TYR C 88 PHE 0.020 0.001 PHE B 286 TRP 0.008 0.001 TRP A 450 HIS 0.010 0.001 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8928) covalent geometry : angle 0.50594 (12081) hydrogen bonds : bond 0.03871 ( 433) hydrogen bonds : angle 4.11306 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 94 time to evaluate : 0.331 Fit side-chains REVERT: C 5 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8113 (mmtm) REVERT: C 70 PHE cc_start: 0.5910 (OUTLIER) cc_final: 0.4952 (t80) REVERT: C 100 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7870 (mtp180) REVERT: C 120 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8066 (mm-40) REVERT: A 157 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8474 (mttm) REVERT: B 110 ASN cc_start: 0.8369 (t0) cc_final: 0.8051 (t0) REVERT: B 157 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8832 (mm) REVERT: B 184 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: B 248 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8599 (t) REVERT: B 290 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6934 (p-80) outliers start: 50 outliers final: 38 residues processed: 134 average time/residue: 0.0798 time to fit residues: 14.8091 Evaluate side-chains 137 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 91 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain D residue 530 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.089112 restraints weight = 14269.385| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.52 r_work: 0.2937 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8928 Z= 0.233 Angle : 0.586 7.774 12081 Z= 0.294 Chirality : 0.043 0.179 1378 Planarity : 0.004 0.046 1537 Dihedral : 4.637 57.464 1187 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.79 % Allowed : 25.41 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.27), residues: 1072 helix: 1.63 (0.22), residues: 541 sheet: -0.87 (0.40), residues: 179 loop : -0.73 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 87 TYR 0.009 0.001 TYR C 88 PHE 0.020 0.002 PHE A 607 TRP 0.005 0.001 TRP A 450 HIS 0.015 0.001 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 8928) covalent geometry : angle 0.58561 (12081) hydrogen bonds : bond 0.04719 ( 433) hydrogen bonds : angle 4.17687 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 98 time to evaluate : 0.318 Fit side-chains REVERT: C 5 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8167 (mmtm) REVERT: C 70 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5014 (t80) REVERT: C 100 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7783 (mtp180) REVERT: C 120 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8043 (mm-40) REVERT: A 157 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8506 (mttm) REVERT: B 110 ASN cc_start: 0.8452 (t0) cc_final: 0.8084 (t0) REVERT: B 157 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8798 (mm) REVERT: B 184 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: B 290 HIS cc_start: 0.7279 (OUTLIER) cc_final: 0.6812 (p-80) outliers start: 56 outliers final: 39 residues processed: 143 average time/residue: 0.0793 time to fit residues: 15.5222 Evaluate side-chains 142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 96 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain D residue 530 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.091736 restraints weight = 14073.762| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.41 r_work: 0.2976 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8928 Z= 0.133 Angle : 0.526 7.003 12081 Z= 0.265 Chirality : 0.040 0.174 1378 Planarity : 0.004 0.046 1537 Dihedral : 4.508 55.544 1187 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.48 % Allowed : 25.83 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.27), residues: 1072 helix: 1.74 (0.23), residues: 541 sheet: -0.81 (0.40), residues: 179 loop : -0.68 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 52 TYR 0.009 0.001 TYR C 88 PHE 0.019 0.001 PHE B 286 TRP 0.008 0.001 TRP A 450 HIS 0.014 0.001 HIS B 290 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8928) covalent geometry : angle 0.52602 (12081) hydrogen bonds : bond 0.04002 ( 433) hydrogen bonds : angle 4.10576 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 96 time to evaluate : 0.218 Fit side-chains REVERT: C 5 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8196 (mmtm) REVERT: C 58 GLU cc_start: 0.8413 (mp0) cc_final: 0.8165 (mp0) REVERT: C 70 PHE cc_start: 0.6224 (OUTLIER) cc_final: 0.5096 (t80) REVERT: C 100 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7889 (mtp180) REVERT: C 120 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8070 (mm-40) REVERT: A 157 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8463 (mttm) REVERT: B 110 ASN cc_start: 0.8416 (t0) cc_final: 0.8067 (t0) REVERT: B 129 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8680 (t0) REVERT: B 157 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8827 (mm) REVERT: B 184 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8236 (mp0) outliers start: 53 outliers final: 37 residues processed: 139 average time/residue: 0.0758 time to fit residues: 14.6494 Evaluate side-chains 139 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 95 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain D residue 530 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.120645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.090477 restraints weight = 14135.061| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.51 r_work: 0.2957 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8928 Z= 0.170 Angle : 0.549 7.044 12081 Z= 0.276 Chirality : 0.041 0.148 1378 Planarity : 0.004 0.046 1537 Dihedral : 4.548 55.619 1187 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.06 % Allowed : 25.62 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.27), residues: 1072 helix: 1.68 (0.22), residues: 541 sheet: -0.84 (0.40), residues: 179 loop : -0.70 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 95 TYR 0.009 0.001 TYR C 88 PHE 0.017 0.001 PHE A 607 TRP 0.008 0.001 TRP A 450 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8928) covalent geometry : angle 0.54897 (12081) hydrogen bonds : bond 0.04259 ( 433) hydrogen bonds : angle 4.10336 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 98 time to evaluate : 0.223 Fit side-chains REVERT: C 5 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8114 (mmtm) REVERT: C 58 GLU cc_start: 0.8438 (mp0) cc_final: 0.8172 (mp0) REVERT: C 70 PHE cc_start: 0.6048 (OUTLIER) cc_final: 0.5034 (t80) REVERT: C 100 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7791 (mtp180) REVERT: C 120 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7981 (mm-40) REVERT: A 157 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8401 (mttm) REVERT: B 110 ASN cc_start: 0.8416 (t0) cc_final: 0.8043 (t0) REVERT: B 157 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8798 (mm) REVERT: B 184 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8085 (mp0) outliers start: 49 outliers final: 40 residues processed: 138 average time/residue: 0.0759 time to fit residues: 14.5479 Evaluate side-chains 140 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 94 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain D residue 530 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.090120 restraints weight = 14132.520| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.51 r_work: 0.2950 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8928 Z= 0.190 Angle : 0.566 8.156 12081 Z= 0.284 Chirality : 0.042 0.149 1378 Planarity : 0.004 0.047 1537 Dihedral : 4.603 56.085 1187 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.17 % Allowed : 25.52 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.27), residues: 1072 helix: 1.63 (0.22), residues: 541 sheet: -0.83 (0.40), residues: 179 loop : -0.76 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 95 TYR 0.009 0.001 TYR C 88 PHE 0.019 0.002 PHE A 607 TRP 0.006 0.001 TRP A 450 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8928) covalent geometry : angle 0.56606 (12081) hydrogen bonds : bond 0.04414 ( 433) hydrogen bonds : angle 4.10969 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 97 time to evaluate : 0.283 Fit side-chains REVERT: C 5 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8149 (mmtm) REVERT: C 70 PHE cc_start: 0.6062 (OUTLIER) cc_final: 0.5091 (t80) REVERT: C 100 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7821 (mtp180) REVERT: C 120 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8031 (mm-40) REVERT: A 157 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8501 (mttm) REVERT: A 247 LEU cc_start: 0.8952 (tp) cc_final: 0.8675 (tp) REVERT: B 110 ASN cc_start: 0.8442 (t0) cc_final: 0.8057 (t0) REVERT: B 129 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8587 (t0) REVERT: B 157 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8805 (mm) REVERT: B 184 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8076 (mp0) outliers start: 50 outliers final: 41 residues processed: 136 average time/residue: 0.0770 time to fit residues: 14.4037 Evaluate side-chains 144 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 817 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain D residue 530 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 0.0770 chunk 18 optimal weight: 0.0970 chunk 106 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.125301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095552 restraints weight = 13951.820| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.51 r_work: 0.3042 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8928 Z= 0.096 Angle : 0.501 7.914 12081 Z= 0.252 Chirality : 0.039 0.138 1378 Planarity : 0.004 0.046 1537 Dihedral : 4.228 49.054 1187 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.10 % Allowed : 27.17 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.27), residues: 1072 helix: 1.85 (0.23), residues: 540 sheet: -0.64 (0.41), residues: 180 loop : -0.74 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 52 TYR 0.007 0.001 TYR B 130 PHE 0.016 0.001 PHE B 286 TRP 0.011 0.001 TRP A 450 HIS 0.001 0.000 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 8928) covalent geometry : angle 0.50117 (12081) hydrogen bonds : bond 0.03074 ( 433) hydrogen bonds : angle 4.03712 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.04 seconds wall clock time: 28 minutes 37.90 seconds (1717.90 seconds total)