Starting phenix.real_space_refine on Sat Aug 23 04:52:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ium_35726/08_2025/8ium_35726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ium_35726/08_2025/8ium_35726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ium_35726/08_2025/8ium_35726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ium_35726/08_2025/8ium_35726.map" model { file = "/net/cci-nas-00/data/ceres_data/8ium_35726/08_2025/8ium_35726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ium_35726/08_2025/8ium_35726.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians S 70 5.16 5 C 6307 2.51 5 N 1716 2.21 5 O 1860 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 9955 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1873 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 4, 'TRANS': 222} Chain breaks: 2 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2591 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2314 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 5, 'TRANS': 287} Chain breaks: 1 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'S2F': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.20, per 1000 atoms: 0.22 Number of scatterers: 9955 At special positions: 0 Unit cell: (122.776, 88.992, 130.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 F 2 9.00 O 1860 8.00 N 1716 7.00 C 6307 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 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " 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: 1.03 Conformation dependent library (CDL) restraints added in 386.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 35.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.588A pdb=" N LYS A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.696A pdb=" N MET A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 removed outlier: 4.219A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.511A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.728A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 316 removed outlier: 3.604A pdb=" N ALA A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 358 Processing helix chain 'B' and resid 9 through 30 removed outlier: 3.838A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.740A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.538A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 86 through 90 removed outlier: 4.003A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 removed outlier: 3.758A pdb=" N ASN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 44 removed outlier: 3.809A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.842A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.535A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 59 removed outlier: 3.956A pdb=" N ARG R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 94 removed outlier: 3.539A pdb=" N SER R 94 " --> pdb=" O PHE R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 102 removed outlier: 3.707A pdb=" N PHE R 101 " --> pdb=" O GLU R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 139 removed outlier: 4.386A pdb=" N SER R 118 " --> pdb=" O CYS R 114 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY R 119 " --> pdb=" O MET R 115 " (cutoff:3.500A) Proline residue: R 122 - end of helix removed outlier: 4.182A pdb=" N GLY R 126 " --> pdb=" O PRO R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 146 Processing helix chain 'R' and resid 148 through 168 Processing helix chain 'R' and resid 170 through 174 removed outlier: 3.939A pdb=" N HIS R 174 " --> pdb=" O ILE R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 233 removed outlier: 4.162A pdb=" N ARG R 199 " --> pdb=" O ASP R 195 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA R 212 " --> pdb=" O LEU R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 276 removed outlier: 3.831A pdb=" N MET R 247 " --> pdb=" O HIS R 243 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS R 259 " --> pdb=" O MET R 255 " (cutoff:3.500A) Proline residue: R 264 - end of helix Processing helix chain 'R' and resid 277 through 279 No H-bonds generated for 'chain 'R' and resid 277 through 279' Processing helix chain 'R' and resid 282 through 305 removed outlier: 4.148A pdb=" N THR R 286 " --> pdb=" O THR R 282 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 323 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.718A pdb=" N LEU A 40 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE A 199 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 42 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N VAL A 201 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N LEU A 44 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ARG A 41 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ILE A 222 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 43 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ASP A 226 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57 removed outlier: 4.655A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER B 336 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 4.124A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 7.103A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 4.306A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR B 164 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA B 172 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 173 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.555A pdb=" N ALA B 213 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR B 226 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU B 215 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.224A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.664A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N CYS B 299 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL B 312 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 301 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.807A pdb=" N ARG E 17 " --> pdb=" O MET E 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 19 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.075A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.668A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG E 160 " --> pdb=" O THR E 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 186 through 187 Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.732A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA N 23 " --> pdb=" O GLN N 5 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER N 7 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.085A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 178 through 179 removed outlier: 3.636A pdb=" N PHE R 187 " --> pdb=" O LYS R 178 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1332 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: 1.53 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1626 1.31 - 1.44: 2811 1.44 - 1.56: 5610 1.56 - 1.68: 3 1.68 - 1.81: 101 Bond restraints: 10151 Sorted by residual: bond pdb=" C10 S2F R 401 " pdb=" C11 S2F R 401 " ideal model delta sigma weight residual 1.529 1.328 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C13 S2F R 401 " pdb=" C14 S2F R 401 " ideal model delta sigma weight residual 1.541 1.352 0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" C11 S2F R 401 " pdb=" C13 S2F R 401 " ideal model delta sigma weight residual 1.534 1.687 -0.153 2.00e-02 2.50e+03 5.84e+01 bond pdb=" CA ILE R 298 " pdb=" C ILE R 298 " ideal model delta sigma weight residual 1.523 1.428 0.095 1.27e-02 6.20e+03 5.61e+01 bond pdb=" CA PHE R 117 " pdb=" C PHE R 117 " ideal model delta sigma weight residual 1.524 1.460 0.065 1.24e-02 6.50e+03 2.71e+01 ... (remaining 10146 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.63: 13680 4.63 - 9.26: 41 9.26 - 13.89: 5 13.89 - 18.52: 0 18.52 - 23.14: 1 Bond angle restraints: 13727 Sorted by residual: angle pdb=" C07 S2F R 401 " pdb=" C08 S2F R 401 " pdb=" C09 S2F R 401 " ideal model delta sigma weight residual 128.15 105.01 23.14 3.00e+00 1.11e-01 5.95e+01 angle pdb=" N LEU R 208 " pdb=" CA LEU R 208 " pdb=" C LEU R 208 " ideal model delta sigma weight residual 113.19 105.13 8.06 1.19e+00 7.06e-01 4.58e+01 angle pdb=" N ALA A 13 " pdb=" CA ALA A 13 " pdb=" C ALA A 13 " ideal model delta sigma weight residual 112.89 104.97 7.92 1.24e+00 6.50e-01 4.07e+01 angle pdb=" N TRP R 295 " pdb=" CA TRP R 295 " pdb=" C TRP R 295 " ideal model delta sigma weight residual 113.23 105.62 7.61 1.24e+00 6.50e-01 3.77e+01 angle pdb=" N ASP R 198 " pdb=" CA ASP R 198 " pdb=" C ASP R 198 " ideal model delta sigma weight residual 111.07 104.52 6.55 1.07e+00 8.73e-01 3.74e+01 ... (remaining 13722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 5833 17.14 - 34.28: 184 34.28 - 51.42: 32 51.42 - 68.56: 6 68.56 - 85.69: 1 Dihedral angle restraints: 6056 sinusoidal: 2389 harmonic: 3667 Sorted by residual: dihedral pdb=" C CYS R 121 " pdb=" N CYS R 121 " pdb=" CA CYS R 121 " pdb=" CB CYS R 121 " ideal model delta harmonic sigma weight residual -122.60 -132.32 9.72 0 2.50e+00 1.60e-01 1.51e+01 dihedral pdb=" C LEU R 203 " pdb=" N LEU R 203 " pdb=" CA LEU R 203 " pdb=" CB LEU R 203 " ideal model delta harmonic sigma weight residual -122.60 -132.22 9.62 0 2.50e+00 1.60e-01 1.48e+01 dihedral pdb=" C ILE R 298 " pdb=" N ILE R 298 " pdb=" CA ILE R 298 " pdb=" CB ILE R 298 " ideal model delta harmonic sigma weight residual -122.00 -112.91 -9.09 0 2.50e+00 1.60e-01 1.32e+01 ... (remaining 6053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1459 0.093 - 0.187: 74 0.187 - 0.280: 6 0.280 - 0.374: 7 0.374 - 0.467: 4 Chirality restraints: 1550 Sorted by residual: chirality pdb=" CA LEU R 203 " pdb=" N LEU R 203 " pdb=" C LEU R 203 " pdb=" CB LEU R 203 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA CYS R 121 " pdb=" N CYS R 121 " pdb=" C CYS R 121 " pdb=" CB CYS R 121 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA LEU R 120 " pdb=" N LEU R 120 " pdb=" C LEU R 120 " pdb=" CB LEU R 120 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 1547 not shown) Planarity restraints: 1739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 294 " 0.040 2.00e-02 2.50e+03 8.07e-02 6.52e+01 pdb=" C THR R 294 " -0.140 2.00e-02 2.50e+03 pdb=" O THR R 294 " 0.054 2.00e-02 2.50e+03 pdb=" N TRP R 295 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS R 121 " 0.076 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO R 122 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO R 122 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO R 122 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 36 " -0.026 2.00e-02 2.50e+03 1.82e-02 6.62e+00 pdb=" CG TYR A 36 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 36 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 36 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 36 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 36 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 36 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 36 " -0.004 2.00e-02 2.50e+03 ... (remaining 1736 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2273 2.79 - 3.32: 9206 3.32 - 3.84: 16078 3.84 - 4.37: 18468 4.37 - 4.90: 32979 Nonbonded interactions: 79004 Sorted by model distance: nonbonded pdb=" OG1 THR B 70 " pdb=" O PRO B 112 " model vdw 2.262 3.040 nonbonded pdb=" N ILE R 298 " pdb=" N LEU R 299 " model vdw 2.278 2.560 nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.286 3.040 nonbonded pdb=" OG SER B 286 " pdb=" OD2 ASP G 47 " model vdw 2.301 3.040 nonbonded pdb=" O GLY R 80 " pdb=" ND2 ASN R 84 " model vdw 2.305 3.120 ... (remaining 78999 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.040 Find NCS groups from input model: 0.050 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 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 0.201 10154 Z= 0.328 Angle : 0.675 23.145 13733 Z= 0.395 Chirality : 0.051 0.467 1550 Planarity : 0.004 0.112 1739 Dihedral : 8.235 85.694 3683 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.16 % Favored : 97.76 % Rotamer: Outliers : 0.28 % Allowed : 4.70 % Favored : 95.02 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.22), residues: 1248 helix: 0.95 (0.25), residues: 406 sheet: -0.74 (0.29), residues: 293 loop : -1.77 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.044 0.001 TYR A 36 PHE 0.020 0.001 PHE R 205 TRP 0.017 0.001 TRP R 295 HIS 0.007 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00531 (10151) covalent geometry : angle 0.67466 (13727) SS BOND : bond 0.00151 ( 3) SS BOND : angle 0.53470 ( 6) hydrogen bonds : bond 0.12545 ( 468) hydrogen bonds : angle 5.06240 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 202 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8070 (mtpp) REVERT: A 226 ASP cc_start: 0.7674 (t0) cc_final: 0.7435 (t0) REVERT: A 343 ASP cc_start: 0.7822 (m-30) cc_final: 0.7590 (m-30) REVERT: A 351 MET cc_start: 0.7475 (ttm) cc_final: 0.7239 (ttp) REVERT: B 267 MET cc_start: 0.7937 (tpp) cc_final: 0.7702 (tpp) REVERT: N 34 MET cc_start: 0.8066 (mmt) cc_final: 0.7823 (mmm) REVERT: R 154 MET cc_start: 0.6408 (mtm) cc_final: 0.6083 (ptt) outliers start: 3 outliers final: 0 residues processed: 204 average time/residue: 0.1002 time to fit residues: 27.9058 Evaluate side-chains 117 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 204 GLN A 234 GLN A 238 ASN B 18 GLN B 93 ASN B 225 GLN B 264 GLN B 271 HIS E 81 GLN E 142 GLN E 167 HIS G 17 GLN N 5 GLN N 120 GLN R 56 GLN R 189 ASN R 250 GLN R 296 ASN R 321 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.201763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.162829 restraints weight = 9903.388| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.54 r_work: 0.3524 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10154 Z= 0.139 Angle : 0.535 8.079 13733 Z= 0.278 Chirality : 0.042 0.154 1550 Planarity : 0.004 0.058 1739 Dihedral : 5.049 44.053 1410 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.57 % Allowed : 8.57 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.24), residues: 1248 helix: 2.02 (0.26), residues: 404 sheet: -0.32 (0.29), residues: 317 loop : -1.12 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 155 TYR 0.013 0.002 TYR E 190 PHE 0.027 0.002 PHE R 78 TRP 0.017 0.002 TRP R 295 HIS 0.006 0.002 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00319 (10151) covalent geometry : angle 0.53448 (13727) SS BOND : bond 0.00155 ( 3) SS BOND : angle 0.74314 ( 6) hydrogen bonds : bond 0.03424 ( 468) hydrogen bonds : angle 4.06154 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.364 Fit side-chains REVERT: A 193 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8206 (mtpp) REVERT: A 226 ASP cc_start: 0.8194 (t0) cc_final: 0.7911 (t0) REVERT: A 260 LYS cc_start: 0.8410 (mttm) cc_final: 0.8209 (mttt) REVERT: A 343 ASP cc_start: 0.8358 (m-30) cc_final: 0.8071 (m-30) REVERT: A 351 MET cc_start: 0.8621 (ttm) cc_final: 0.8290 (ttp) REVERT: B 279 THR cc_start: 0.9158 (m) cc_final: 0.8642 (p) REVERT: E 17 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7593 (ttm-80) REVERT: E 75 LYS cc_start: 0.7674 (ptmt) cc_final: 0.7327 (ptpp) REVERT: E 77 THR cc_start: 0.7908 (t) cc_final: 0.7704 (m) REVERT: N 34 MET cc_start: 0.8242 (mmt) cc_final: 0.7759 (mmm) outliers start: 17 outliers final: 10 residues processed: 173 average time/residue: 0.1260 time to fit residues: 28.7144 Evaluate side-chains 130 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain R residue 259 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 106 optimal weight: 0.0980 chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 327 HIS A 336 ASN B 264 GLN E 34 HIS E 81 GLN N 53 GLN ** R 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 189 ASN R 244 HIS R 297 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.181861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141707 restraints weight = 9848.290| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.65 r_work: 0.3133 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10154 Z= 0.164 Angle : 0.560 8.220 13733 Z= 0.293 Chirality : 0.043 0.167 1550 Planarity : 0.004 0.071 1739 Dihedral : 4.980 47.683 1410 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.21 % Allowed : 12.17 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.24), residues: 1248 helix: 2.10 (0.25), residues: 404 sheet: -0.16 (0.28), residues: 329 loop : -0.64 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 339 TYR 0.018 0.002 TYR E 190 PHE 0.019 0.002 PHE B 297 TRP 0.015 0.002 TRP R 295 HIS 0.006 0.002 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00386 (10151) covalent geometry : angle 0.56005 (13727) SS BOND : bond 0.00254 ( 3) SS BOND : angle 0.76554 ( 6) hydrogen bonds : bond 0.04075 ( 468) hydrogen bonds : angle 4.31777 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.415 Fit side-chains REVERT: A 192 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8293 (m-30) REVERT: A 193 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8152 (mtpp) REVERT: A 351 MET cc_start: 0.8798 (ttm) cc_final: 0.8397 (ttp) REVERT: B 169 THR cc_start: 0.8637 (m) cc_final: 0.8427 (p) REVERT: G 20 MET cc_start: 0.5741 (mpp) cc_final: 0.5418 (mpp) REVERT: G 45 LYS cc_start: 0.7237 (mmtm) cc_final: 0.6834 (mtmm) REVERT: N 34 MET cc_start: 0.8184 (mmt) cc_final: 0.7884 (mmm) REVERT: R 62 SER cc_start: 0.7842 (t) cc_final: 0.7620 (p) REVERT: R 74 VAL cc_start: 0.8116 (t) cc_final: 0.7844 (m) outliers start: 24 outliers final: 14 residues processed: 154 average time/residue: 0.1044 time to fit residues: 21.9727 Evaluate side-chains 135 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 297 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 0.0030 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN E 81 GLN G 58 ASN R 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.185544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.145226 restraints weight = 9865.417| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.61 r_work: 0.3277 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10154 Z= 0.105 Angle : 0.464 6.961 13733 Z= 0.245 Chirality : 0.040 0.143 1550 Planarity : 0.004 0.063 1739 Dihedral : 5.052 65.800 1410 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.21 % Allowed : 12.53 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.24), residues: 1248 helix: 2.48 (0.26), residues: 404 sheet: 0.07 (0.29), residues: 321 loop : -0.55 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 37 TYR 0.013 0.001 TYR E 190 PHE 0.013 0.001 PHE A 189 TRP 0.012 0.001 TRP R 295 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00238 (10151) covalent geometry : angle 0.46453 (13727) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.36967 ( 6) hydrogen bonds : bond 0.03329 ( 468) hydrogen bonds : angle 4.04481 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.287 Fit side-chains REVERT: A 192 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: A 193 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8098 (mtpp) REVERT: A 197 HIS cc_start: 0.7668 (m-70) cc_final: 0.7287 (m-70) REVERT: A 351 MET cc_start: 0.8714 (ttm) cc_final: 0.8299 (ttp) REVERT: B 219 ARG cc_start: 0.8259 (mmt90) cc_final: 0.8011 (mpt-90) REVERT: E 16 SER cc_start: 0.7532 (t) cc_final: 0.7256 (t) REVERT: G 45 LYS cc_start: 0.7145 (mmtm) cc_final: 0.6934 (ptpp) REVERT: N 59 SER cc_start: 0.6088 (m) cc_final: 0.5835 (p) outliers start: 24 outliers final: 15 residues processed: 144 average time/residue: 0.0865 time to fit residues: 17.0485 Evaluate side-chains 139 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 297 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 GLN R 81 HIS R 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.171967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126580 restraints weight = 10157.030| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.00 r_work: 0.3070 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10154 Z= 0.115 Angle : 0.468 7.278 13733 Z= 0.247 Chirality : 0.040 0.140 1550 Planarity : 0.004 0.058 1739 Dihedral : 4.852 78.896 1410 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.95 % Allowed : 12.44 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.24), residues: 1248 helix: 2.60 (0.26), residues: 402 sheet: 0.11 (0.28), residues: 333 loop : -0.42 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 17 TYR 0.015 0.001 TYR E 190 PHE 0.013 0.001 PHE A 189 TRP 0.011 0.001 TRP R 295 HIS 0.004 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00266 (10151) covalent geometry : angle 0.46833 (13727) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.35393 ( 6) hydrogen bonds : bond 0.03400 ( 468) hydrogen bonds : angle 4.06915 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.271 Fit side-chains REVERT: A 192 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: A 193 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8467 (mtmm) REVERT: A 197 HIS cc_start: 0.7894 (m-70) cc_final: 0.7502 (m-70) REVERT: A 321 ARG cc_start: 0.8043 (ptp90) cc_final: 0.7745 (ptp90) REVERT: A 351 MET cc_start: 0.8807 (ttm) cc_final: 0.8385 (ttp) REVERT: B 219 ARG cc_start: 0.8350 (mmt90) cc_final: 0.8033 (mpt-90) REVERT: E 16 SER cc_start: 0.7596 (t) cc_final: 0.7378 (t) REVERT: E 58 TYR cc_start: 0.8212 (m-80) cc_final: 0.7959 (m-10) REVERT: G 20 MET cc_start: 0.5997 (mpp) cc_final: 0.5447 (mpp) REVERT: G 45 LYS cc_start: 0.7301 (mmtm) cc_final: 0.6958 (ptpp) REVERT: N 59 SER cc_start: 0.5911 (m) cc_final: 0.5671 (p) outliers start: 32 outliers final: 22 residues processed: 145 average time/residue: 0.1002 time to fit residues: 19.7186 Evaluate side-chains 143 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 297 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 75 optimal weight: 20.0000 chunk 76 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 GLN R 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.175863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.137083 restraints weight = 10115.216| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.82 r_work: 0.2987 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10154 Z= 0.163 Angle : 0.532 8.530 13733 Z= 0.279 Chirality : 0.042 0.175 1550 Planarity : 0.004 0.056 1739 Dihedral : 5.170 96.729 1410 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.95 % Allowed : 12.72 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.24), residues: 1248 helix: 2.46 (0.25), residues: 400 sheet: 0.08 (0.29), residues: 328 loop : -0.36 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 17 TYR 0.021 0.001 TYR E 190 PHE 0.016 0.002 PHE A 189 TRP 0.011 0.002 TRP R 262 HIS 0.006 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00388 (10151) covalent geometry : angle 0.53235 (13727) SS BOND : bond 0.00270 ( 3) SS BOND : angle 0.49483 ( 6) hydrogen bonds : bond 0.03986 ( 468) hydrogen bonds : angle 4.30455 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.399 Fit side-chains REVERT: A 16 LYS cc_start: 0.8372 (mtpt) cc_final: 0.8114 (mttp) REVERT: A 192 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: A 193 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8117 (mtpp) REVERT: A 197 HIS cc_start: 0.7796 (m-70) cc_final: 0.7365 (m-70) REVERT: A 321 ARG cc_start: 0.7992 (ptp90) cc_final: 0.7690 (ptp90) REVERT: A 351 MET cc_start: 0.8815 (ttm) cc_final: 0.8376 (ttp) REVERT: B 219 ARG cc_start: 0.8266 (mmt90) cc_final: 0.7960 (mpt-90) REVERT: B 223 CYS cc_start: 0.8624 (p) cc_final: 0.8300 (p) REVERT: B 225 GLN cc_start: 0.8888 (mt0) cc_final: 0.8435 (mt0) REVERT: E 16 SER cc_start: 0.7804 (t) cc_final: 0.7601 (t) REVERT: E 58 TYR cc_start: 0.8394 (m-80) cc_final: 0.8174 (m-10) REVERT: G 45 LYS cc_start: 0.7376 (mmtm) cc_final: 0.6967 (ptpp) REVERT: N 59 SER cc_start: 0.5917 (m) cc_final: 0.5652 (p) REVERT: R 74 VAL cc_start: 0.8064 (t) cc_final: 0.7756 (m) outliers start: 32 outliers final: 25 residues processed: 144 average time/residue: 0.1053 time to fit residues: 20.5069 Evaluate side-chains 144 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 GLN R 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.167895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.121619 restraints weight = 10129.442| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.92 r_work: 0.3031 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10154 Z= 0.114 Angle : 0.480 7.203 13733 Z= 0.253 Chirality : 0.040 0.167 1550 Planarity : 0.004 0.052 1739 Dihedral : 5.043 99.661 1410 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.86 % Allowed : 13.09 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.24), residues: 1248 helix: 2.69 (0.25), residues: 400 sheet: 0.12 (0.29), residues: 328 loop : -0.34 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 17 TYR 0.015 0.001 TYR E 190 PHE 0.013 0.001 PHE A 189 TRP 0.010 0.001 TRP R 295 HIS 0.004 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00259 (10151) covalent geometry : angle 0.48035 (13727) SS BOND : bond 0.00202 ( 3) SS BOND : angle 0.39818 ( 6) hydrogen bonds : bond 0.03470 ( 468) hydrogen bonds : angle 4.11782 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.264 Fit side-chains REVERT: A 193 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8156 (mtpp) REVERT: A 197 HIS cc_start: 0.7569 (m-70) cc_final: 0.7231 (m-70) REVERT: A 351 MET cc_start: 0.8750 (ttm) cc_final: 0.8314 (ttp) REVERT: B 219 ARG cc_start: 0.8279 (mmt90) cc_final: 0.8062 (mpt-90) REVERT: B 223 CYS cc_start: 0.8614 (p) cc_final: 0.8328 (p) REVERT: B 225 GLN cc_start: 0.8872 (mt0) cc_final: 0.8509 (mt0) REVERT: E 16 SER cc_start: 0.7729 (t) cc_final: 0.7524 (t) REVERT: G 45 LYS cc_start: 0.7308 (mmtm) cc_final: 0.7094 (ptpp) REVERT: N 59 SER cc_start: 0.6156 (m) cc_final: 0.5924 (p) REVERT: R 74 VAL cc_start: 0.8189 (t) cc_final: 0.7937 (m) REVERT: R 129 MET cc_start: 0.8157 (mtp) cc_final: 0.7957 (mtp) outliers start: 31 outliers final: 25 residues processed: 143 average time/residue: 0.0952 time to fit residues: 18.9569 Evaluate side-chains 140 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 297 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 57 optimal weight: 0.0470 chunk 25 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 GLN R 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.170900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.125650 restraints weight = 10113.960| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.86 r_work: 0.3081 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10154 Z= 0.100 Angle : 0.473 10.056 13733 Z= 0.247 Chirality : 0.040 0.165 1550 Planarity : 0.003 0.050 1739 Dihedral : 4.930 100.245 1410 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.58 % Allowed : 13.73 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.24), residues: 1248 helix: 2.82 (0.25), residues: 400 sheet: 0.10 (0.29), residues: 339 loop : -0.27 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 17 TYR 0.014 0.001 TYR E 58 PHE 0.012 0.001 PHE A 189 TRP 0.010 0.001 TRP A 211 HIS 0.003 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00222 (10151) covalent geometry : angle 0.47268 (13727) SS BOND : bond 0.00173 ( 3) SS BOND : angle 0.36679 ( 6) hydrogen bonds : bond 0.03249 ( 468) hydrogen bonds : angle 4.03342 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.249 Fit side-chains REVERT: A 193 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8153 (mtpp) REVERT: A 197 HIS cc_start: 0.7545 (m-70) cc_final: 0.7216 (m-70) REVERT: B 223 CYS cc_start: 0.8601 (p) cc_final: 0.8360 (p) REVERT: B 225 GLN cc_start: 0.8844 (mt0) cc_final: 0.8510 (mt0) REVERT: N 59 SER cc_start: 0.6100 (m) cc_final: 0.5877 (p) REVERT: R 53 LYS cc_start: 0.7694 (mttt) cc_final: 0.7270 (mmtt) REVERT: R 74 VAL cc_start: 0.8109 (t) cc_final: 0.7877 (m) outliers start: 28 outliers final: 24 residues processed: 144 average time/residue: 0.0914 time to fit residues: 18.2683 Evaluate side-chains 141 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 184 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 0.0000 chunk 61 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 GLN R 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.171798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.126885 restraints weight = 10056.936| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.83 r_work: 0.3141 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10154 Z= 0.099 Angle : 0.475 12.087 13733 Z= 0.247 Chirality : 0.040 0.165 1550 Planarity : 0.004 0.048 1739 Dihedral : 4.722 93.457 1410 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.49 % Allowed : 14.75 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.24), residues: 1248 helix: 2.87 (0.25), residues: 400 sheet: 0.19 (0.29), residues: 328 loop : -0.27 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 307 TYR 0.012 0.001 TYR E 190 PHE 0.012 0.001 PHE A 189 TRP 0.010 0.001 TRP A 211 HIS 0.003 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00220 (10151) covalent geometry : angle 0.47555 (13727) SS BOND : bond 0.00173 ( 3) SS BOND : angle 0.35332 ( 6) hydrogen bonds : bond 0.03176 ( 468) hydrogen bonds : angle 3.99113 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.369 Fit side-chains REVERT: A 193 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8136 (mtpp) REVERT: A 197 HIS cc_start: 0.7505 (m-70) cc_final: 0.7200 (m-70) REVERT: B 219 ARG cc_start: 0.8025 (mmm-85) cc_final: 0.7641 (mpt-90) REVERT: B 225 GLN cc_start: 0.8828 (mt0) cc_final: 0.8536 (mt0) REVERT: E 160 ARG cc_start: 0.7497 (ttm110) cc_final: 0.7248 (ttm-80) REVERT: R 53 LYS cc_start: 0.7677 (mttt) cc_final: 0.7244 (mmtt) REVERT: R 74 VAL cc_start: 0.8096 (t) cc_final: 0.7865 (m) outliers start: 27 outliers final: 24 residues processed: 138 average time/residue: 0.0992 time to fit residues: 18.9541 Evaluate side-chains 137 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 259 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 17 GLN R 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.161983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.116742 restraints weight = 10112.736| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.91 r_work: 0.3016 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10154 Z= 0.191 Angle : 0.583 10.370 13733 Z= 0.303 Chirality : 0.044 0.181 1550 Planarity : 0.004 0.049 1739 Dihedral : 5.339 103.669 1410 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.21 % Allowed : 15.48 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.24), residues: 1248 helix: 2.54 (0.25), residues: 397 sheet: 0.12 (0.29), residues: 318 loop : -0.44 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 307 TYR 0.025 0.002 TYR E 190 PHE 0.017 0.002 PHE A 189 TRP 0.014 0.002 TRP R 262 HIS 0.007 0.002 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00462 (10151) covalent geometry : angle 0.58252 (13727) SS BOND : bond 0.00332 ( 3) SS BOND : angle 0.65307 ( 6) hydrogen bonds : bond 0.04266 ( 468) hydrogen bonds : angle 4.40566 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.397 Fit side-chains REVERT: A 16 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8364 (mttp) REVERT: A 193 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8201 (mtpp) REVERT: A 197 HIS cc_start: 0.8037 (m-70) cc_final: 0.7634 (m-70) REVERT: A 241 LYS cc_start: 0.8639 (tttt) cc_final: 0.8401 (ttmt) REVERT: B 219 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7792 (mpp80) REVERT: B 225 GLN cc_start: 0.8975 (mt0) cc_final: 0.8666 (mt0) REVERT: E 158 SER cc_start: 0.8853 (t) cc_final: 0.8403 (p) REVERT: E 160 ARG cc_start: 0.7673 (ttm110) cc_final: 0.7423 (ttm-80) REVERT: R 74 VAL cc_start: 0.8276 (t) cc_final: 0.7936 (m) REVERT: R 297 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: R 314 ASN cc_start: 0.7189 (t0) cc_final: 0.6930 (t0) outliers start: 24 outliers final: 22 residues processed: 145 average time/residue: 0.1042 time to fit residues: 20.9055 Evaluate side-chains 145 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 297 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 0.0070 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.165588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.121264 restraints weight = 10262.044| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.90 r_work: 0.2994 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.6250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10154 Z= 0.111 Angle : 0.522 9.579 13733 Z= 0.273 Chirality : 0.041 0.169 1550 Planarity : 0.004 0.049 1739 Dihedral : 5.216 103.749 1410 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.94 % Allowed : 16.31 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.24), residues: 1248 helix: 2.74 (0.25), residues: 397 sheet: 0.11 (0.29), residues: 324 loop : -0.37 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 307 TYR 0.019 0.001 TYR E 190 PHE 0.015 0.001 PHE A 185 TRP 0.010 0.001 TRP R 295 HIS 0.003 0.001 HIS R 243 Details of bonding type rmsd covalent geometry : bond 0.00247 (10151) covalent geometry : angle 0.52182 (13727) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.55460 ( 6) hydrogen bonds : bond 0.03667 ( 468) hydrogen bonds : angle 4.26662 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.92 seconds wall clock time: 42 minutes 38.96 seconds (2558.96 seconds total)