Starting phenix.real_space_refine on Sat Aug 23 01:47:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3v_41013/08_2025/8t3v_41013_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3v_41013/08_2025/8t3v_41013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t3v_41013/08_2025/8t3v_41013_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3v_41013/08_2025/8t3v_41013_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t3v_41013/08_2025/8t3v_41013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3v_41013/08_2025/8t3v_41013.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 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 52 5.16 5 C 5562 2.51 5 N 1507 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8742 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1790 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2061 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 19, 'TRANS': 256} Chain breaks: 1 Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'CLR': 1, 'HXA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.26, per 1000 atoms: 0.26 Number of scatterers: 8742 At special positions: 0 Unit cell: (86.73, 120.596, 123.9, 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 52 16.00 O 1621 8.00 N 1507 7.00 C 5562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.04 Simple disulfide: pdb=" SG CYS R 79 " - pdb=" SG CYS R 170 " distance=2.03 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: 0.84 Conformation dependent library (CDL) restraints added in 357.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 38.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.657A pdb=" N THR A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 45 removed outlier: 4.079A pdb=" N GLY A 45 " --> pdb=" O ASP A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 45' Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.632A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 99 " --> pdb=" O TRP A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.508A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.639A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.020A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 4.083A pdb=" N ARG A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 203 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.790A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.722A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.827A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.035A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 225 removed outlier: 3.508A pdb=" N VAL N 225 " --> pdb=" O ALA N 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 37 Proline residue: R 21 - end of helix removed outlier: 3.810A pdb=" N LEU R 25 " --> pdb=" O PRO R 21 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS R 33 " --> pdb=" O GLY R 29 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 57 Processing helix chain 'R' and resid 57 through 68 removed outlier: 4.203A pdb=" N LEU R 61 " --> pdb=" O VAL R 57 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 110 removed outlier: 4.179A pdb=" N VAL R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL R 84 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Proline residue: R 89 - end of helix removed outlier: 4.192A pdb=" N GLY R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 117 removed outlier: 3.679A pdb=" N ALA R 116 " --> pdb=" O LEU R 112 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE R 117 " --> pdb=" O GLY R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 145 removed outlier: 3.984A pdb=" N SER R 123 " --> pdb=" O ARG R 119 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU R 135 " --> pdb=" O TRP R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 191 removed outlier: 3.583A pdb=" N GLY R 180 " --> pdb=" O PRO R 176 " (cutoff:3.500A) Proline residue: R 181 - end of helix removed outlier: 3.586A pdb=" N LEU R 186 " --> pdb=" O ALA R 182 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE R 191 " --> pdb=" O SER R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 212 removed outlier: 3.859A pdb=" N ARG R 211 " --> pdb=" O ARG R 207 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER R 212 " --> pdb=" O ALA R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 236 removed outlier: 3.654A pdb=" N TRP R 224 " --> pdb=" O LEU R 220 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL R 225 " --> pdb=" O ARG R 221 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA R 229 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 250 removed outlier: 4.157A pdb=" N TYR R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN R 244 " --> pdb=" O TYR R 240 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL R 245 " --> pdb=" O ASN R 241 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE R 248 " --> pdb=" O ASN R 244 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU R 249 " --> pdb=" O VAL R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 267 removed outlier: 3.565A pdb=" N ILE R 263 " --> pdb=" O LYS R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 277 removed outlier: 3.718A pdb=" N LEU R 271 " --> pdb=" O TRP R 267 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.866A pdb=" N GLY R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76 removed outlier: 3.705A pdb=" N PHE A 74 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 142 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.421A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.690A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.205A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151 removed outlier: 6.416A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.663A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.658A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.744A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.706A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.070A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.070A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG N 98 " --> pdb=" O PHE N 110 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 141 through 142 removed outlier: 3.680A pdb=" N VAL N 156 " --> pdb=" O ILE N 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 147 through 149 removed outlier: 3.787A pdb=" N GLY N 226 " --> pdb=" O LEU N 246 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR N 176 " --> pdb=" O MET N 231 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU N 175 " --> pdb=" O TYR N 191 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR N 191 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP N 177 " --> pdb=" O LEU N 189 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1152 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: 1.45 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2820 1.34 - 1.46: 1434 1.46 - 1.58: 4610 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8936 Sorted by residual: bond pdb=" N VAL N 225 " pdb=" CA VAL N 225 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.19e-02 7.06e+03 1.12e+01 bond pdb=" N VAL A 109 " pdb=" CA VAL A 109 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.10e-02 8.26e+03 1.09e+01 bond pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.06e+01 bond pdb=" N CYS B 149 " pdb=" CA CYS B 149 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.23e-02 6.61e+03 1.00e+01 bond pdb=" N PHE N 68 " pdb=" CA PHE N 68 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.21e-02 6.83e+03 9.98e+00 ... (remaining 8931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 11846 2.53 - 5.07: 264 5.07 - 7.60: 23 7.60 - 10.14: 4 10.14 - 12.67: 1 Bond angle restraints: 12138 Sorted by residual: angle pdb=" CA ILE A 107 " pdb=" C ILE A 107 " pdb=" N PHE A 108 " ideal model delta sigma weight residual 115.25 122.32 -7.07 9.50e-01 1.11e+00 5.54e+01 angle pdb=" O ILE A 107 " pdb=" C ILE A 107 " pdb=" N PHE A 108 " ideal model delta sigma weight residual 121.96 115.79 6.17 8.40e-01 1.42e+00 5.40e+01 angle pdb=" C PHE B 151 " pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " ideal model delta sigma weight residual 110.19 103.47 6.72 1.62e+00 3.81e-01 1.72e+01 angle pdb=" C ARG N 192 " pdb=" N MET N 193 " pdb=" CA MET N 193 " ideal model delta sigma weight residual 121.54 129.46 -7.92 1.91e+00 2.74e-01 1.72e+01 angle pdb=" C GLN N 82 " pdb=" N MET N 83 " pdb=" CA MET N 83 " ideal model delta sigma weight residual 121.86 115.34 6.52 1.58e+00 4.01e-01 1.70e+01 ... (remaining 12133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4626 17.81 - 35.63: 532 35.63 - 53.44: 133 53.44 - 71.26: 21 71.26 - 89.07: 3 Dihedral angle restraints: 5315 sinusoidal: 2056 harmonic: 3259 Sorted by residual: dihedral pdb=" C CYS B 233 " pdb=" N CYS B 233 " pdb=" CA CYS B 233 " pdb=" CB CYS B 233 " ideal model delta harmonic sigma weight residual -122.60 -113.27 -9.33 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CB CYS N 160 " pdb=" SG CYS N 160 " pdb=" SG CYS N 230 " pdb=" CB CYS N 230 " ideal model delta sinusoidal sigma weight residual 93.00 61.99 31.01 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA MET N 231 " pdb=" C MET N 231 " pdb=" N GLN N 232 " pdb=" CA GLN N 232 " ideal model delta harmonic sigma weight residual 180.00 162.74 17.26 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 5312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1065 0.053 - 0.106: 225 0.106 - 0.160: 57 0.160 - 0.213: 15 0.213 - 0.266: 6 Chirality restraints: 1368 Sorted by residual: chirality pdb=" CA LEU B 152 " pdb=" N LEU B 152 " pdb=" C LEU B 152 " pdb=" CB LEU B 152 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LEU A 36 " pdb=" N LEU A 36 " pdb=" C LEU A 36 " pdb=" CB LEU A 36 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA LEU N 79 " pdb=" N LEU N 79 " pdb=" C LEU N 79 " pdb=" CB LEU N 79 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1365 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 HXA R 302 " 0.066 2.00e-02 2.50e+03 1.25e-01 1.57e+02 pdb=" C16 HXA R 302 " -0.165 2.00e-02 2.50e+03 pdb=" C17 HXA R 302 " 0.164 2.00e-02 2.50e+03 pdb=" C18 HXA R 302 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 HXA R 302 " 0.109 2.00e-02 2.50e+03 1.10e-01 1.21e+02 pdb=" C4 HXA R 302 " -0.106 2.00e-02 2.50e+03 pdb=" C5 HXA R 302 " -0.114 2.00e-02 2.50e+03 pdb=" C6 HXA R 302 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 HXA R 302 " -0.041 2.00e-02 2.50e+03 7.44e-02 5.54e+01 pdb=" C7 HXA R 302 " 0.097 2.00e-02 2.50e+03 pdb=" C8 HXA R 302 " -0.097 2.00e-02 2.50e+03 pdb=" C9 HXA R 302 " 0.041 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 397 2.72 - 3.26: 8853 3.26 - 3.81: 14304 3.81 - 4.35: 17536 4.35 - 4.90: 29965 Nonbonded interactions: 71055 Sorted by model distance: nonbonded pdb=" O TYR R 240 " pdb=" OG SER R 243 " model vdw 2.175 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.229 3.040 nonbonded pdb=" NH1 ARG A 93 " pdb=" OD1 ASP A 124 " model vdw 2.279 3.120 nonbonded pdb=" O THR B 47 " pdb=" OG1 THR B 47 " model vdw 2.286 3.040 ... (remaining 71050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.040 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.000 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 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 : 0.005 0.044 8939 Z= 0.328 Angle : 0.809 12.674 12144 Z= 0.509 Chirality : 0.053 0.266 1368 Planarity : 0.007 0.125 1555 Dihedral : 15.857 89.070 3214 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.44 % Allowed : 25.66 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.25), residues: 1120 helix: 1.36 (0.28), residues: 350 sheet: -0.41 (0.32), residues: 263 loop : -0.03 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 72 TYR 0.017 0.001 TYR B 59 PHE 0.020 0.001 PHE B 151 TRP 0.014 0.001 TRP B 339 HIS 0.005 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8936) covalent geometry : angle 0.80831 (12138) SS BOND : bond 0.00465 ( 3) SS BOND : angle 1.58174 ( 6) hydrogen bonds : bond 0.24081 ( 404) hydrogen bonds : angle 8.23452 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 225 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 TYR cc_start: 0.7495 (m-80) cc_final: 0.7011 (m-80) REVERT: B 217 MET cc_start: 0.6921 (tpt) cc_final: 0.6685 (tpt) REVERT: N 34 MET cc_start: 0.4780 (mmt) cc_final: 0.4238 (mmt) REVERT: N 76 LYS cc_start: 0.7339 (mtpp) cc_final: 0.6758 (mppt) REVERT: N 173 THR cc_start: 0.4018 (m) cc_final: 0.3806 (m) REVERT: R 8 SER cc_start: 0.7843 (m) cc_final: 0.7388 (t) REVERT: R 28 ARG cc_start: 0.7049 (ttp-170) cc_final: 0.6776 (mmt180) REVERT: R 35 ARG cc_start: 0.5935 (mmm160) cc_final: 0.5725 (mmp-170) outliers start: 4 outliers final: 0 residues processed: 227 average time/residue: 0.0881 time to fit residues: 27.8126 Evaluate side-chains 170 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS N 168 HIS N 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.186207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131705 restraints weight = 10675.739| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.07 r_work: 0.3486 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8939 Z= 0.158 Angle : 0.655 13.387 12144 Z= 0.331 Chirality : 0.044 0.154 1368 Planarity : 0.005 0.053 1555 Dihedral : 4.900 39.237 1312 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.04 % Allowed : 23.91 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.25), residues: 1120 helix: 1.64 (0.28), residues: 359 sheet: -0.32 (0.33), residues: 246 loop : 0.04 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 192 TYR 0.017 0.002 TYR N 191 PHE 0.026 0.002 PHE B 199 TRP 0.019 0.002 TRP B 297 HIS 0.008 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8936) covalent geometry : angle 0.65450 (12138) SS BOND : bond 0.00408 ( 3) SS BOND : angle 1.09321 ( 6) hydrogen bonds : bond 0.04336 ( 404) hydrogen bonds : angle 5.35373 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6323 (ptt) REVERT: A 124 ASP cc_start: 0.8390 (t0) cc_final: 0.7963 (t70) REVERT: B 57 LYS cc_start: 0.8657 (ptpp) cc_final: 0.8182 (pttm) REVERT: B 124 TYR cc_start: 0.8322 (m-80) cc_final: 0.7726 (m-80) REVERT: B 325 MET cc_start: 0.8222 (mmt) cc_final: 0.7972 (tpp) REVERT: N 71 SER cc_start: 0.7518 (p) cc_final: 0.7266 (m) REVERT: N 76 LYS cc_start: 0.7168 (mtpp) cc_final: 0.6907 (mppt) REVERT: N 108 PHE cc_start: 0.7743 (m-80) cc_final: 0.7427 (m-80) REVERT: R 8 SER cc_start: 0.7710 (m) cc_final: 0.7394 (t) REVERT: R 28 ARG cc_start: 0.7050 (ttp-170) cc_final: 0.6048 (mmp-170) REVERT: R 74 LEU cc_start: 0.8170 (mm) cc_final: 0.7810 (tp) outliers start: 37 outliers final: 16 residues processed: 204 average time/residue: 0.0715 time to fit residues: 21.6634 Evaluate side-chains 163 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 168 HIS Chi-restraints excluded: chain N residue 217 ILE Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 180 GLN R 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.195442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147000 restraints weight = 10664.147| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 3.29 r_work: 0.3612 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8939 Z= 0.132 Angle : 0.602 11.268 12144 Z= 0.301 Chirality : 0.042 0.142 1368 Planarity : 0.004 0.047 1555 Dihedral : 4.721 48.397 1312 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.17 % Allowed : 25.22 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.26), residues: 1120 helix: 1.80 (0.28), residues: 365 sheet: -0.38 (0.30), residues: 271 loop : 0.05 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.015 0.001 TYR N 191 PHE 0.016 0.001 PHE B 199 TRP 0.018 0.001 TRP R 131 HIS 0.025 0.002 HIS N 168 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8936) covalent geometry : angle 0.60216 (12138) SS BOND : bond 0.00756 ( 3) SS BOND : angle 0.93418 ( 6) hydrogen bonds : bond 0.03775 ( 404) hydrogen bonds : angle 4.79480 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6729 (ptt) REVERT: A 124 ASP cc_start: 0.8514 (t0) cc_final: 0.8288 (t70) REVERT: A 151 GLU cc_start: 0.8164 (pp20) cc_final: 0.7927 (pt0) REVERT: B 57 LYS cc_start: 0.8681 (ptpp) cc_final: 0.8336 (pttm) REVERT: B 124 TYR cc_start: 0.8488 (m-80) cc_final: 0.8167 (m-80) REVERT: B 215 GLU cc_start: 0.7192 (tt0) cc_final: 0.6781 (tt0) REVERT: N 76 LYS cc_start: 0.7280 (mtpp) cc_final: 0.6927 (mppt) REVERT: N 83 MET cc_start: 0.6404 (mmm) cc_final: 0.5998 (mmt) REVERT: N 93 MET cc_start: 0.7331 (ttm) cc_final: 0.7090 (ttm) REVERT: R 28 ARG cc_start: 0.7066 (ttp-170) cc_final: 0.5949 (mmp-170) REVERT: R 35 ARG cc_start: 0.6402 (mmm160) cc_final: 0.5400 (mmp-170) REVERT: R 74 LEU cc_start: 0.8268 (mm) cc_final: 0.7955 (tp) REVERT: R 184 PHE cc_start: 0.6602 (t80) cc_final: 0.6393 (t80) outliers start: 29 outliers final: 11 residues processed: 191 average time/residue: 0.0791 time to fit residues: 21.6909 Evaluate side-chains 159 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 217 ILE Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 275 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 30.0000 chunk 73 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS N 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.180105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125064 restraints weight = 10806.006| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.08 r_work: 0.3400 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8939 Z= 0.140 Angle : 0.601 13.529 12144 Z= 0.300 Chirality : 0.043 0.169 1368 Planarity : 0.004 0.038 1555 Dihedral : 4.803 59.780 1312 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.49 % Allowed : 25.44 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.26), residues: 1120 helix: 1.83 (0.28), residues: 370 sheet: -0.26 (0.31), residues: 268 loop : -0.03 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 38 TYR 0.018 0.001 TYR N 191 PHE 0.025 0.002 PHE N 213 TRP 0.017 0.001 TRP R 131 HIS 0.014 0.002 HIS N 168 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8936) covalent geometry : angle 0.60114 (12138) SS BOND : bond 0.00378 ( 3) SS BOND : angle 1.09654 ( 6) hydrogen bonds : bond 0.03338 ( 404) hydrogen bonds : angle 4.57636 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7975 (pm20) cc_final: 0.6884 (tp30) REVERT: B 66 ASP cc_start: 0.8251 (t0) cc_final: 0.7835 (t0) REVERT: B 124 TYR cc_start: 0.8690 (m-80) cc_final: 0.8122 (m-80) REVERT: B 217 MET cc_start: 0.8161 (ptp) cc_final: 0.7919 (ptt) REVERT: N 39 GLN cc_start: 0.7806 (tt0) cc_final: 0.7380 (tt0) REVERT: N 71 SER cc_start: 0.8355 (p) cc_final: 0.8059 (m) REVERT: N 76 LYS cc_start: 0.7587 (mtpp) cc_final: 0.7156 (mppt) REVERT: N 83 MET cc_start: 0.7360 (mmm) cc_final: 0.6983 (mmm) REVERT: N 93 MET cc_start: 0.7883 (ttm) cc_final: 0.7548 (ttm) REVERT: R 28 ARG cc_start: 0.6998 (ttp-170) cc_final: 0.5833 (mmp-170) REVERT: R 35 ARG cc_start: 0.6430 (mmm160) cc_final: 0.5369 (mmp-170) REVERT: R 74 LEU cc_start: 0.8207 (mm) cc_final: 0.7912 (tp) REVERT: R 119 ARG cc_start: 0.6909 (mtp180) cc_final: 0.6681 (mtm-85) REVERT: R 184 PHE cc_start: 0.6752 (t80) cc_final: 0.6481 (t80) REVERT: R 253 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7216 (mt) outliers start: 32 outliers final: 22 residues processed: 191 average time/residue: 0.0992 time to fit residues: 26.2961 Evaluate side-chains 178 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 217 ILE Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 22 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.178993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.123733 restraints weight = 10761.959| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.16 r_work: 0.3384 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.6582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8939 Z= 0.123 Angle : 0.578 12.719 12144 Z= 0.290 Chirality : 0.042 0.222 1368 Planarity : 0.003 0.034 1555 Dihedral : 4.672 59.819 1312 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.60 % Allowed : 25.22 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.26), residues: 1120 helix: 2.06 (0.28), residues: 362 sheet: -0.18 (0.31), residues: 271 loop : 0.06 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 35 TYR 0.019 0.001 TYR N 191 PHE 0.014 0.001 PHE B 199 TRP 0.017 0.001 TRP R 131 HIS 0.004 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8936) covalent geometry : angle 0.57779 (12138) SS BOND : bond 0.00353 ( 3) SS BOND : angle 0.76797 ( 6) hydrogen bonds : bond 0.03095 ( 404) hydrogen bonds : angle 4.38268 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ASN cc_start: 0.8603 (m-40) cc_final: 0.7980 (t0) REVERT: B 124 TYR cc_start: 0.8600 (m-80) cc_final: 0.8223 (m-80) REVERT: B 170 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: B 311 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.8248 (t-90) REVERT: B 316 SER cc_start: 0.8924 (t) cc_final: 0.8698 (p) REVERT: N 39 GLN cc_start: 0.7794 (tt0) cc_final: 0.7541 (tt0) REVERT: N 71 SER cc_start: 0.8427 (p) cc_final: 0.8091 (m) REVERT: N 76 LYS cc_start: 0.7654 (mtpp) cc_final: 0.7167 (mppt) REVERT: N 83 MET cc_start: 0.7704 (mmm) cc_final: 0.7462 (mmm) REVERT: N 93 MET cc_start: 0.7926 (ttm) cc_final: 0.7583 (ttm) REVERT: R 28 ARG cc_start: 0.6972 (ttp-170) cc_final: 0.5743 (mmp-170) REVERT: R 35 ARG cc_start: 0.6575 (mmm160) cc_final: 0.5435 (mmp-170) REVERT: R 253 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7205 (mt) outliers start: 33 outliers final: 22 residues processed: 193 average time/residue: 0.1023 time to fit residues: 27.2752 Evaluate side-chains 174 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 217 ILE Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 51 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS N 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.178409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125476 restraints weight = 10650.577| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.39 r_work: 0.3365 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.7105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8939 Z= 0.122 Angle : 0.586 11.146 12144 Z= 0.293 Chirality : 0.042 0.209 1368 Planarity : 0.003 0.032 1555 Dihedral : 4.603 56.845 1312 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.80 % Allowed : 25.22 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.26), residues: 1120 helix: 2.16 (0.28), residues: 361 sheet: -0.16 (0.32), residues: 262 loop : 0.01 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 35 TYR 0.021 0.001 TYR N 191 PHE 0.019 0.001 PHE R 16 TRP 0.018 0.001 TRP R 131 HIS 0.004 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8936) covalent geometry : angle 0.58636 (12138) SS BOND : bond 0.00391 ( 3) SS BOND : angle 0.76788 ( 6) hydrogen bonds : bond 0.02977 ( 404) hydrogen bonds : angle 4.29853 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7990 (pm20) cc_final: 0.7115 (tp30) REVERT: A 244 ASN cc_start: 0.8538 (m-40) cc_final: 0.7982 (t0) REVERT: B 124 TYR cc_start: 0.8614 (m-80) cc_final: 0.8146 (m-80) REVERT: B 153 ASP cc_start: 0.7673 (m-30) cc_final: 0.7342 (m-30) REVERT: B 170 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: B 311 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.8081 (t-90) REVERT: G 47 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7128 (mt-10) REVERT: N 76 LYS cc_start: 0.7704 (mtpp) cc_final: 0.7168 (mppt) REVERT: N 83 MET cc_start: 0.8038 (mmm) cc_final: 0.7768 (mmt) REVERT: R 28 ARG cc_start: 0.7011 (ttp-170) cc_final: 0.5760 (mmp-170) REVERT: R 35 ARG cc_start: 0.6725 (mmm160) cc_final: 0.5579 (mmp-170) REVERT: R 253 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7263 (mt) outliers start: 44 outliers final: 28 residues processed: 196 average time/residue: 0.0968 time to fit residues: 26.1075 Evaluate side-chains 189 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 156 VAL Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 217 ILE Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 25 optimal weight: 0.0170 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 0.0980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 168 HIS N 180 GLN ** R 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.180339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126130 restraints weight = 10733.715| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.02 r_work: 0.3408 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.7372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8939 Z= 0.106 Angle : 0.578 13.924 12144 Z= 0.284 Chirality : 0.041 0.171 1368 Planarity : 0.003 0.030 1555 Dihedral : 4.413 52.651 1312 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.82 % Allowed : 25.87 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.26), residues: 1120 helix: 2.17 (0.28), residues: 362 sheet: 0.03 (0.32), residues: 279 loop : 0.09 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.017 0.001 TYR N 191 PHE 0.013 0.001 PHE B 199 TRP 0.019 0.001 TRP R 131 HIS 0.004 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8936) covalent geometry : angle 0.57842 (12138) SS BOND : bond 0.00356 ( 3) SS BOND : angle 0.64411 ( 6) hydrogen bonds : bond 0.02811 ( 404) hydrogen bonds : angle 4.18726 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7993 (pm20) cc_final: 0.7377 (tp30) REVERT: A 244 ASN cc_start: 0.8474 (m-40) cc_final: 0.7913 (t0) REVERT: B 124 TYR cc_start: 0.8528 (m-80) cc_final: 0.8099 (m-80) REVERT: B 153 ASP cc_start: 0.7624 (m-30) cc_final: 0.7298 (m-30) REVERT: B 170 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: B 198 LEU cc_start: 0.8778 (mp) cc_final: 0.8436 (mt) REVERT: B 217 MET cc_start: 0.8085 (ptp) cc_final: 0.7853 (ptt) REVERT: B 311 HIS cc_start: 0.8522 (OUTLIER) cc_final: 0.8098 (t-90) REVERT: N 68 PHE cc_start: 0.6912 (m-10) cc_final: 0.6656 (m-10) REVERT: N 73 ASP cc_start: 0.6440 (t70) cc_final: 0.5938 (t70) REVERT: N 76 LYS cc_start: 0.7665 (mtpp) cc_final: 0.7241 (mppt) REVERT: N 83 MET cc_start: 0.8073 (mmm) cc_final: 0.7802 (mmt) REVERT: R 28 ARG cc_start: 0.7079 (ttp-170) cc_final: 0.5802 (mmp-170) REVERT: R 35 ARG cc_start: 0.6743 (mmm160) cc_final: 0.5575 (mmp-170) REVERT: R 253 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7286 (mt) outliers start: 35 outliers final: 21 residues processed: 188 average time/residue: 0.0991 time to fit residues: 25.8778 Evaluate side-chains 182 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 156 VAL Chi-restraints excluded: chain N residue 217 ILE Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 241 ASN Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.176838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123731 restraints weight = 10658.277| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.30 r_work: 0.3337 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.7757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8939 Z= 0.128 Angle : 0.594 12.233 12144 Z= 0.294 Chirality : 0.042 0.157 1368 Planarity : 0.003 0.032 1555 Dihedral : 4.483 51.632 1312 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.71 % Allowed : 25.98 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.26), residues: 1120 helix: 2.17 (0.28), residues: 362 sheet: 0.01 (0.32), residues: 267 loop : 0.10 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.017 0.001 TYR N 191 PHE 0.015 0.001 PHE R 9 TRP 0.020 0.001 TRP R 131 HIS 0.005 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8936) covalent geometry : angle 0.59414 (12138) SS BOND : bond 0.00268 ( 3) SS BOND : angle 0.65015 ( 6) hydrogen bonds : bond 0.02866 ( 404) hydrogen bonds : angle 4.19245 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.8196 (ttm) cc_final: 0.7866 (ttm) REVERT: A 166 GLU cc_start: 0.8068 (pm20) cc_final: 0.7368 (tp30) REVERT: A 230 ASP cc_start: 0.8596 (m-30) cc_final: 0.8235 (m-30) REVERT: A 244 ASN cc_start: 0.8487 (m-40) cc_final: 0.7951 (t0) REVERT: B 124 TYR cc_start: 0.8608 (m-80) cc_final: 0.8168 (m-80) REVERT: B 153 ASP cc_start: 0.7690 (m-30) cc_final: 0.7361 (m-30) REVERT: B 170 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: B 198 LEU cc_start: 0.8781 (mp) cc_final: 0.8527 (mt) REVERT: B 217 MET cc_start: 0.8139 (ptp) cc_final: 0.7888 (ptt) REVERT: B 311 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8059 (t-90) REVERT: G 47 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7668 (tm-30) REVERT: N 68 PHE cc_start: 0.7262 (m-10) cc_final: 0.6674 (m-10) REVERT: N 73 ASP cc_start: 0.6594 (t70) cc_final: 0.5991 (t70) REVERT: N 76 LYS cc_start: 0.7771 (mtpp) cc_final: 0.7364 (mppt) REVERT: N 83 MET cc_start: 0.8249 (mmm) cc_final: 0.7878 (mmt) REVERT: N 193 MET cc_start: 0.7995 (ptt) cc_final: 0.7746 (ptt) REVERT: R 9 PHE cc_start: 0.8363 (t80) cc_final: 0.8045 (t80) REVERT: R 35 ARG cc_start: 0.6810 (mmm160) cc_final: 0.5665 (mmp-170) REVERT: R 253 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7330 (mt) outliers start: 34 outliers final: 25 residues processed: 182 average time/residue: 0.0931 time to fit residues: 23.9667 Evaluate side-chains 179 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 156 VAL Chi-restraints excluded: chain N residue 217 ILE Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 20 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 272 ASN ** 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 = 0.4077 r_free = 0.4077 target = 0.171859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.116288 restraints weight = 10701.019| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.10 r_work: 0.3283 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.8283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8939 Z= 0.172 Angle : 0.636 11.937 12144 Z= 0.317 Chirality : 0.044 0.160 1368 Planarity : 0.004 0.036 1555 Dihedral : 4.752 52.471 1312 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.38 % Allowed : 26.53 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.26), residues: 1120 helix: 2.04 (0.28), residues: 362 sheet: -0.10 (0.32), residues: 265 loop : 0.07 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.020 0.001 TYR B 59 PHE 0.028 0.002 PHE R 16 TRP 0.020 0.001 TRP R 131 HIS 0.004 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8936) covalent geometry : angle 0.63639 (12138) SS BOND : bond 0.00278 ( 3) SS BOND : angle 0.68682 ( 6) hydrogen bonds : bond 0.03132 ( 404) hydrogen bonds : angle 4.36468 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8114 (pm20) cc_final: 0.7436 (tp30) REVERT: A 244 ASN cc_start: 0.8512 (m-40) cc_final: 0.7991 (t0) REVERT: B 124 TYR cc_start: 0.8774 (m-80) cc_final: 0.8218 (m-80) REVERT: B 153 ASP cc_start: 0.7699 (m-30) cc_final: 0.7386 (m-30) REVERT: B 170 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: B 198 LEU cc_start: 0.8639 (mp) cc_final: 0.8399 (mt) REVERT: B 217 MET cc_start: 0.8202 (ptp) cc_final: 0.7950 (ptt) REVERT: B 266 HIS cc_start: 0.8676 (t-90) cc_final: 0.8448 (t-90) REVERT: B 311 HIS cc_start: 0.8803 (OUTLIER) cc_final: 0.8056 (t-90) REVERT: N 87 ARG cc_start: 0.6833 (ptp90) cc_final: 0.5598 (ptp90) REVERT: R 9 PHE cc_start: 0.8474 (t80) cc_final: 0.8108 (t80) REVERT: R 35 ARG cc_start: 0.6682 (mmm160) cc_final: 0.5630 (mmp-170) outliers start: 31 outliers final: 24 residues processed: 176 average time/residue: 0.0974 time to fit residues: 24.1284 Evaluate side-chains 174 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 156 VAL Chi-restraints excluded: chain N residue 217 ILE Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 66 optimal weight: 0.0970 chunk 57 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 168 HIS ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 HIS ** R 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.172418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119157 restraints weight = 10687.108| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.38 r_work: 0.3287 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.8492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8939 Z= 0.155 Angle : 0.646 11.688 12144 Z= 0.318 Chirality : 0.043 0.155 1368 Planarity : 0.004 0.035 1555 Dihedral : 4.731 50.736 1312 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.17 % Allowed : 26.64 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.26), residues: 1120 helix: 2.05 (0.27), residues: 363 sheet: -0.13 (0.32), residues: 265 loop : 0.12 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.019 0.001 TYR N 191 PHE 0.015 0.001 PHE R 9 TRP 0.020 0.001 TRP R 131 HIS 0.004 0.001 HIS R 216 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8936) covalent geometry : angle 0.64593 (12138) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.65329 ( 6) hydrogen bonds : bond 0.02984 ( 404) hydrogen bonds : angle 4.30265 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8094 (pm20) cc_final: 0.7434 (tp30) REVERT: A 244 ASN cc_start: 0.8488 (m-40) cc_final: 0.7998 (t0) REVERT: B 124 TYR cc_start: 0.8698 (m-80) cc_final: 0.8186 (m-80) REVERT: B 153 ASP cc_start: 0.7669 (m-30) cc_final: 0.7364 (m-30) REVERT: B 170 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7937 (m-30) REVERT: B 198 LEU cc_start: 0.8640 (mp) cc_final: 0.8383 (mt) REVERT: B 217 MET cc_start: 0.8207 (ptp) cc_final: 0.7945 (ptt) REVERT: B 266 HIS cc_start: 0.8649 (t-90) cc_final: 0.8340 (t-90) REVERT: B 311 HIS cc_start: 0.8748 (OUTLIER) cc_final: 0.8003 (t-90) REVERT: N 68 PHE cc_start: 0.7281 (m-10) cc_final: 0.6994 (m-80) REVERT: R 35 ARG cc_start: 0.6725 (mmm160) cc_final: 0.5662 (mmp-170) REVERT: R 253 LEU cc_start: 0.7852 (tt) cc_final: 0.7561 (mt) outliers start: 29 outliers final: 25 residues processed: 179 average time/residue: 0.1014 time to fit residues: 25.1946 Evaluate side-chains 178 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 156 VAL Chi-restraints excluded: chain N residue 217 ILE Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 168 HIS ** R 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.174715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121229 restraints weight = 10583.273| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.37 r_work: 0.3313 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.8627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8939 Z= 0.121 Angle : 0.611 11.606 12144 Z= 0.300 Chirality : 0.042 0.146 1368 Planarity : 0.004 0.030 1555 Dihedral : 4.588 47.773 1312 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.95 % Allowed : 26.75 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.26), residues: 1120 helix: 2.17 (0.28), residues: 362 sheet: -0.19 (0.32), residues: 269 loop : 0.18 (0.30), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 241 TYR 0.022 0.001 TYR N 191 PHE 0.029 0.001 PHE R 16 TRP 0.021 0.001 TRP R 131 HIS 0.004 0.001 HIS R 137 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8936) covalent geometry : angle 0.61138 (12138) SS BOND : bond 0.00233 ( 3) SS BOND : angle 0.58736 ( 6) hydrogen bonds : bond 0.02793 ( 404) hydrogen bonds : angle 4.19024 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2234.88 seconds wall clock time: 39 minutes 10.97 seconds (2350.97 seconds total)