Starting phenix.real_space_refine on Wed Apr 30 19:14:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ium_35726/04_2025/8ium_35726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ium_35726/04_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_35726/04_2025/8ium_35726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ium_35726/04_2025/8ium_35726.map" model { file = "/net/cci-nas-00/data/ceres_data/8ium_35726/04_2025/8ium_35726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ium_35726/04_2025/8ium_35726.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.69, per 1000 atoms: 0.57 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.21 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: 3.38 Time building geometry restraints manager: 2.81 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.920 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.560 ------------------------------------------------------------------------------- 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 : 6.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.001 TRP R 295 HIS 0.007 0.001 HIS B 59 PHE 0.020 0.001 PHE R 205 TYR 0.044 0.001 TYR A 36 ARG 0.002 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.12545 ( 468) hydrogen bonds : angle 5.06240 ( 1332) SS BOND : bond 0.00151 ( 3) SS BOND : angle 0.53470 ( 6) covalent geometry : bond 0.00531 (10151) covalent geometry : angle 0.67466 (13727) *********************** 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 : 1.117 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: 0.6084 (ptt) outliers start: 3 outliers final: 0 residues processed: 204 average time/residue: 0.2546 time to fit residues: 70.0537 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 : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 238 ASN A 327 HIS B 18 GLN B 93 ASN B 225 GLN B 271 HIS E 34 HIS E 81 GLN E 142 GLN E 167 HIS G 17 GLN N 5 GLN N 120 GLN R 56 GLN R 244 HIS ** R 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 ASN R 321 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.184759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.146790 restraints weight = 9842.953| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.70 r_work: 0.3220 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10154 Z= 0.228 Angle : 0.675 9.631 13733 Z= 0.351 Chirality : 0.047 0.211 1550 Planarity : 0.005 0.075 1739 Dihedral : 5.695 67.883 1410 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.94 % Allowed : 8.66 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.23), residues: 1248 helix: 1.53 (0.25), residues: 404 sheet: -0.43 (0.28), residues: 328 loop : -1.13 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 262 HIS 0.008 0.002 HIS R 243 PHE 0.025 0.003 PHE R 117 TYR 0.027 0.002 TYR E 190 ARG 0.007 0.001 ARG E 191 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 468) hydrogen bonds : angle 4.65194 ( 1332) SS BOND : bond 0.00275 ( 3) SS BOND : angle 1.04847 ( 6) covalent geometry : bond 0.00537 (10151) covalent geometry : angle 0.67506 (13727) *********************** 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 178 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8187 (mtpp) REVERT: A 308 LYS cc_start: 0.8015 (tptt) cc_final: 0.7679 (ttpt) REVERT: A 351 MET cc_start: 0.8764 (ttm) cc_final: 0.8408 (ttp) REVERT: B 252 ASP cc_start: 0.6659 (t0) cc_final: 0.6315 (t0) REVERT: E 16 SER cc_start: 0.8121 (m) cc_final: 0.7782 (t) REVERT: E 17 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7779 (ttm-80) REVERT: N 34 MET cc_start: 0.8247 (mmt) cc_final: 0.7958 (mmm) REVERT: R 74 VAL cc_start: 0.8219 (t) cc_final: 0.7915 (m) REVERT: R 155 MET cc_start: 0.7194 (ptp) cc_final: 0.6983 (ptt) outliers start: 21 outliers final: 12 residues processed: 174 average time/residue: 0.3271 time to fit residues: 73.4621 Evaluate side-chains 132 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 56 LEU Chi-restraints excluded: chain B residue 151 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 30 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain R residue 184 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 61 optimal weight: 8.9990 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 103 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 245 ASN E 194 ASN G 58 ASN ** R 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.188805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.148845 restraints weight = 9893.176| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.58 r_work: 0.3349 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4667 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= 0.100 Angle : 0.472 7.711 13733 Z= 0.249 Chirality : 0.040 0.155 1550 Planarity : 0.004 0.068 1739 Dihedral : 4.497 45.026 1410 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.47 % Allowed : 11.24 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.24), residues: 1248 helix: 2.33 (0.26), residues: 404 sheet: -0.13 (0.28), residues: 328 loop : -0.68 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 295 HIS 0.006 0.001 HIS A 197 PHE 0.016 0.001 PHE R 78 TYR 0.012 0.001 TYR A 36 ARG 0.004 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 468) hydrogen bonds : angle 4.08908 ( 1332) SS BOND : bond 0.00152 ( 3) SS BOND : angle 0.33827 ( 6) covalent geometry : bond 0.00217 (10151) covalent geometry : angle 0.47182 (13727) *********************** 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 146 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 1.157 Fit side-chains REVERT: A 193 LYS cc_start: 0.8667 (ttmm) cc_final: 0.8228 (mtpp) REVERT: A 197 HIS cc_start: 0.7768 (m-70) cc_final: 0.7394 (m-70) REVERT: A 237 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8446 (mp) REVERT: B 219 ARG cc_start: 0.8057 (mpt-90) cc_final: 0.7577 (mmp-170) REVERT: E 16 SER cc_start: 0.7962 (m) cc_final: 0.7631 (t) REVERT: G 45 LYS cc_start: 0.7085 (mmtm) cc_final: 0.6872 (mtmm) REVERT: N 34 MET cc_start: 0.8247 (mmt) cc_final: 0.7994 (mmm) outliers start: 16 outliers final: 9 residues processed: 143 average time/residue: 0.2623 time to fit residues: 50.3324 Evaluate side-chains 129 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 29 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 80 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN G 58 ASN ** R 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.171990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.125729 restraints weight = 10017.339| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.97 r_work: 0.3053 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10154 Z= 0.134 Angle : 0.502 7.723 13733 Z= 0.264 Chirality : 0.041 0.164 1550 Planarity : 0.004 0.065 1739 Dihedral : 4.719 48.758 1410 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.40 % Allowed : 11.89 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1248 helix: 2.54 (0.26), residues: 402 sheet: -0.02 (0.28), residues: 328 loop : -0.48 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 295 HIS 0.012 0.001 HIS A 197 PHE 0.016 0.002 PHE A 189 TYR 0.021 0.001 TYR E 190 ARG 0.004 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 468) hydrogen bonds : angle 4.14738 ( 1332) SS BOND : bond 0.00229 ( 3) SS BOND : angle 0.51642 ( 6) covalent geometry : bond 0.00313 (10151) covalent geometry : angle 0.50229 (13727) *********************** 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 157 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.991 Fit side-chains REVERT: A 193 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8150 (mtpp) REVERT: A 321 ARG cc_start: 0.8087 (ptp90) cc_final: 0.7771 (ptp90) REVERT: B 219 ARG cc_start: 0.8173 (mpt-90) cc_final: 0.7933 (mpt-90) REVERT: B 223 CYS cc_start: 0.8633 (p) cc_final: 0.8307 (p) REVERT: B 248 THR cc_start: 0.8691 (p) cc_final: 0.8437 (p) REVERT: E 16 SER cc_start: 0.8078 (m) cc_final: 0.7742 (t) REVERT: E 186 GLN cc_start: 0.8530 (tt0) cc_final: 0.8182 (tt0) REVERT: G 20 MET cc_start: 0.5895 (mpp) cc_final: 0.5431 (mpp) REVERT: G 45 LYS cc_start: 0.7299 (mmtm) cc_final: 0.6920 (ptpp) REVERT: N 34 MET cc_start: 0.8150 (mmt) cc_final: 0.7920 (mmm) REVERT: N 59 SER cc_start: 0.5867 (m) cc_final: 0.5594 (p) outliers start: 26 outliers final: 17 residues processed: 151 average time/residue: 0.2507 time to fit residues: 50.9566 Evaluate side-chains 144 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 183 THR 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 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 82 optimal weight: 0.0370 chunk 123 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 80 GLN E 81 GLN ** R 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.174850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129624 restraints weight = 9984.361| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.85 r_work: 0.3191 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10154 Z= 0.099 Angle : 0.454 6.318 13733 Z= 0.242 Chirality : 0.040 0.166 1550 Planarity : 0.003 0.057 1739 Dihedral : 4.758 62.678 1410 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.21 % Allowed : 13.36 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1248 helix: 2.80 (0.26), residues: 402 sheet: 0.15 (0.29), residues: 322 loop : -0.37 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 295 HIS 0.007 0.001 HIS A 197 PHE 0.013 0.001 PHE A 189 TYR 0.015 0.001 TYR E 190 ARG 0.006 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 468) hydrogen bonds : angle 3.98670 ( 1332) SS BOND : bond 0.00183 ( 3) SS BOND : angle 0.34878 ( 6) covalent geometry : bond 0.00219 (10151) covalent geometry : angle 0.45447 (13727) *********************** 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 148 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.019 Fit side-chains REVERT: A 193 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8473 (mtmm) REVERT: A 198 MET cc_start: 0.9008 (ttp) cc_final: 0.8730 (ttp) REVERT: B 219 ARG cc_start: 0.8157 (mpt-90) cc_final: 0.7950 (mpt-90) REVERT: B 225 GLN cc_start: 0.8897 (mt0) cc_final: 0.8479 (mt0) REVERT: B 248 THR cc_start: 0.8597 (p) cc_final: 0.8336 (p) REVERT: B 308 ASP cc_start: 0.8007 (m-30) cc_final: 0.7471 (p0) REVERT: E 16 SER cc_start: 0.8070 (m) cc_final: 0.7790 (t) REVERT: E 186 GLN cc_start: 0.8476 (tt0) cc_final: 0.8116 (tt0) REVERT: G 45 LYS cc_start: 0.7209 (mmtm) cc_final: 0.6984 (ptpp) REVERT: N 59 SER cc_start: 0.5956 (m) cc_final: 0.5696 (p) outliers start: 24 outliers final: 16 residues processed: 142 average time/residue: 0.3055 time to fit residues: 58.6141 Evaluate side-chains 138 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 56 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 22 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 20 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** R 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 250 GLN R 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.172863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.132113 restraints weight = 10055.466| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.74 r_work: 0.3010 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10154 Z= 0.214 Angle : 0.592 8.039 13733 Z= 0.312 Chirality : 0.045 0.193 1550 Planarity : 0.004 0.059 1739 Dihedral : 5.164 84.573 1410 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.76 % Allowed : 12.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1248 helix: 2.46 (0.25), residues: 400 sheet: 0.04 (0.29), residues: 318 loop : -0.43 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 87 HIS 0.013 0.002 HIS A 197 PHE 0.018 0.002 PHE A 189 TYR 0.028 0.002 TYR E 190 ARG 0.006 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 468) hydrogen bonds : angle 4.49890 ( 1332) SS BOND : bond 0.00345 ( 3) SS BOND : angle 0.55615 ( 6) covalent geometry : bond 0.00519 (10151) covalent geometry : angle 0.59204 (13727) *********************** 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 162 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.049 Fit side-chains REVERT: A 193 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8163 (mtpp) REVERT: A 197 HIS cc_start: 0.7855 (m-70) cc_final: 0.7445 (m-70) REVERT: A 228 SER cc_start: 0.8274 (t) cc_final: 0.8023 (p) REVERT: A 351 MET cc_start: 0.8989 (ttm) cc_final: 0.8534 (ttp) REVERT: B 219 ARG cc_start: 0.8194 (mpt-90) cc_final: 0.7852 (mpt-90) REVERT: B 223 CYS cc_start: 0.8686 (p) cc_final: 0.8331 (p) REVERT: B 225 GLN cc_start: 0.8948 (mt0) cc_final: 0.8563 (mt0) REVERT: B 248 THR cc_start: 0.8773 (p) cc_final: 0.8464 (p) REVERT: E 16 SER cc_start: 0.8528 (m) cc_final: 0.8217 (t) REVERT: E 17 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7805 (ttm-80) REVERT: E 58 TYR cc_start: 0.8259 (m-10) cc_final: 0.7981 (m-10) REVERT: E 158 SER cc_start: 0.8869 (t) cc_final: 0.8413 (p) REVERT: G 45 LYS cc_start: 0.7490 (mmtm) cc_final: 0.7073 (ptpp) REVERT: N 59 SER cc_start: 0.6024 (m) cc_final: 0.5689 (p) REVERT: R 74 VAL cc_start: 0.8227 (t) cc_final: 0.7844 (m) REVERT: R 314 ASN cc_start: 0.7173 (t0) cc_final: 0.6898 (t0) outliers start: 30 outliers final: 24 residues processed: 153 average time/residue: 0.2377 time to fit residues: 49.7852 Evaluate side-chains 151 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 279 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 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 199 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 71 SER Chi-restraints excluded: chain R residue 297 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 101 optimal weight: 0.0030 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.170828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126757 restraints weight = 10221.556| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.86 r_work: 0.3056 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10154 Z= 0.119 Angle : 0.487 6.949 13733 Z= 0.259 Chirality : 0.041 0.156 1550 Planarity : 0.004 0.052 1739 Dihedral : 4.932 91.274 1410 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.21 % Allowed : 13.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.24), residues: 1248 helix: 2.68 (0.26), residues: 402 sheet: 0.17 (0.29), residues: 322 loop : -0.41 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 295 HIS 0.007 0.001 HIS A 197 PHE 0.014 0.001 PHE A 189 TYR 0.019 0.001 TYR E 190 ARG 0.007 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 468) hydrogen bonds : angle 4.20016 ( 1332) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.42740 ( 6) covalent geometry : bond 0.00274 (10151) covalent geometry : angle 0.48731 (13727) *********************** 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 153 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.094 Fit side-chains REVERT: A 197 HIS cc_start: 0.7656 (m-70) cc_final: 0.7358 (m-70) REVERT: B 219 ARG cc_start: 0.8206 (mpt-90) cc_final: 0.7933 (mpp80) REVERT: B 223 CYS cc_start: 0.8605 (p) cc_final: 0.8346 (p) REVERT: B 225 GLN cc_start: 0.8890 (mt0) cc_final: 0.8575 (mt0) REVERT: B 248 THR cc_start: 0.8603 (p) cc_final: 0.8308 (p) REVERT: B 308 ASP cc_start: 0.7976 (m-30) cc_final: 0.7393 (p0) REVERT: E 16 SER cc_start: 0.8426 (m) cc_final: 0.8143 (t) REVERT: E 17 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7855 (ttm-80) REVERT: E 58 TYR cc_start: 0.7899 (m-10) cc_final: 0.7626 (m-10) REVERT: E 158 SER cc_start: 0.8780 (t) cc_final: 0.8324 (p) REVERT: G 45 LYS cc_start: 0.7352 (mmtm) cc_final: 0.7095 (ptpp) REVERT: N 59 SER cc_start: 0.6012 (m) cc_final: 0.5743 (p) REVERT: R 74 VAL cc_start: 0.8185 (t) cc_final: 0.7888 (m) REVERT: R 314 ASN cc_start: 0.7173 (t0) cc_final: 0.6907 (t0) outliers start: 24 outliers final: 20 residues processed: 147 average time/residue: 0.2763 time to fit residues: 54.8712 Evaluate side-chains 141 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 71 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 102 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 81 HIS 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 = 0.168216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.123437 restraints weight = 10179.399| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.79 r_work: 0.3114 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10154 Z= 0.116 Angle : 0.477 6.750 13733 Z= 0.254 Chirality : 0.040 0.163 1550 Planarity : 0.004 0.051 1739 Dihedral : 4.840 87.510 1410 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.49 % Allowed : 13.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1248 helix: 2.79 (0.25), residues: 401 sheet: 0.12 (0.29), residues: 326 loop : -0.30 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 295 HIS 0.005 0.001 HIS A 197 PHE 0.014 0.001 PHE A 189 TYR 0.017 0.001 TYR E 190 ARG 0.008 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 468) hydrogen bonds : angle 4.11342 ( 1332) SS BOND : bond 0.00207 ( 3) SS BOND : angle 0.43409 ( 6) covalent geometry : bond 0.00266 (10151) covalent geometry : angle 0.47713 (13727) *********************** 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 152 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.005 Fit side-chains REVERT: A 197 HIS cc_start: 0.7633 (m-70) cc_final: 0.7333 (m-70) REVERT: A 198 MET cc_start: 0.8975 (ttp) cc_final: 0.8688 (ttp) REVERT: B 225 GLN cc_start: 0.8847 (mt0) cc_final: 0.8545 (mt0) REVERT: B 248 THR cc_start: 0.8510 (p) cc_final: 0.8217 (p) REVERT: B 308 ASP cc_start: 0.8020 (m-30) cc_final: 0.7365 (p0) REVERT: E 16 SER cc_start: 0.8330 (m) cc_final: 0.8092 (t) REVERT: E 158 SER cc_start: 0.8732 (t) cc_final: 0.8289 (p) REVERT: G 45 LYS cc_start: 0.7316 (mmtm) cc_final: 0.7089 (ptpp) REVERT: N 59 SER cc_start: 0.6172 (m) cc_final: 0.5945 (p) REVERT: R 74 VAL cc_start: 0.8145 (t) cc_final: 0.7858 (m) REVERT: R 129 MET cc_start: 0.7992 (mtp) cc_final: 0.7782 (mtp) REVERT: R 314 ASN cc_start: 0.7242 (t0) cc_final: 0.7009 (t0) outliers start: 27 outliers final: 23 residues processed: 144 average time/residue: 0.2551 time to fit residues: 50.0358 Evaluate side-chains 142 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 279 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 66 ARG Chi-restraints excluded: chain E residue 82 MET 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 71 SER 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 104 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.168510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.125062 restraints weight = 10155.845| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.76 r_work: 0.3060 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10154 Z= 0.151 Angle : 0.528 9.698 13733 Z= 0.278 Chirality : 0.042 0.170 1550 Planarity : 0.004 0.051 1739 Dihedral : 5.052 91.702 1410 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.03 % Allowed : 14.47 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1248 helix: 2.67 (0.25), residues: 399 sheet: 0.10 (0.29), residues: 326 loop : -0.35 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 295 HIS 0.009 0.001 HIS A 197 PHE 0.015 0.001 PHE A 189 TYR 0.023 0.001 TYR E 190 ARG 0.006 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 468) hydrogen bonds : angle 4.27491 ( 1332) SS BOND : bond 0.00280 ( 3) SS BOND : angle 0.54748 ( 6) covalent geometry : bond 0.00359 (10151) covalent geometry : angle 0.52791 (13727) *********************** 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 147 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.160 Fit side-chains REVERT: A 197 HIS cc_start: 0.7994 (m-70) cc_final: 0.7728 (m-70) REVERT: B 219 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.7768 (mpp80) REVERT: B 225 GLN cc_start: 0.8963 (mt0) cc_final: 0.8708 (mt0) REVERT: B 248 THR cc_start: 0.8693 (p) cc_final: 0.8444 (p) REVERT: B 308 ASP cc_start: 0.8218 (m-30) cc_final: 0.7580 (p0) REVERT: E 16 SER cc_start: 0.8492 (m) cc_final: 0.8251 (t) REVERT: E 58 TYR cc_start: 0.8206 (m-10) cc_final: 0.7823 (m-10) REVERT: E 158 SER cc_start: 0.8835 (t) cc_final: 0.8382 (p) REVERT: G 45 LYS cc_start: 0.7459 (mmtm) cc_final: 0.7051 (ptpp) REVERT: N 59 SER cc_start: 0.6264 (m) cc_final: 0.6054 (p) REVERT: R 74 VAL cc_start: 0.8239 (t) cc_final: 0.7894 (m) REVERT: R 129 MET cc_start: 0.8223 (mtp) cc_final: 0.7979 (mtp) REVERT: R 314 ASN cc_start: 0.7309 (t0) cc_final: 0.7057 (t0) outliers start: 22 outliers final: 22 residues processed: 143 average time/residue: 0.2525 time to fit residues: 49.8360 Evaluate side-chains 144 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 85 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 71 SER Chi-restraints excluded: chain R residue 184 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.176207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134985 restraints weight = 10061.730| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.71 r_work: 0.3041 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10154 Z= 0.119 Angle : 0.490 7.069 13733 Z= 0.261 Chirality : 0.041 0.168 1550 Planarity : 0.004 0.049 1739 Dihedral : 4.949 90.284 1410 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.30 % Allowed : 14.56 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.24), residues: 1248 helix: 2.67 (0.25), residues: 405 sheet: 0.19 (0.29), residues: 320 loop : -0.33 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 295 HIS 0.005 0.001 HIS A 197 PHE 0.014 0.001 PHE A 189 TYR 0.017 0.001 TYR E 190 ARG 0.007 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 468) hydrogen bonds : angle 4.16366 ( 1332) SS BOND : bond 0.00227 ( 3) SS BOND : angle 0.48763 ( 6) covalent geometry : bond 0.00274 (10151) covalent geometry : angle 0.49012 (13727) ********************** 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: 25 poor density : 125 time to evaluate : 1.176 Fit side-chains REVERT: A 197 HIS cc_start: 0.7722 (m-70) cc_final: 0.7377 (m-70) REVERT: A 198 MET cc_start: 0.9093 (ttp) cc_final: 0.8815 (ttp) REVERT: B 202 ARG cc_start: 0.7867 (mmt-90) cc_final: 0.7515 (mmt180) REVERT: B 219 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7655 (mpp80) REVERT: B 225 GLN cc_start: 0.8846 (mt0) cc_final: 0.8603 (mt0) REVERT: B 248 THR cc_start: 0.8549 (p) cc_final: 0.8236 (p) REVERT: B 308 ASP cc_start: 0.7972 (m-30) cc_final: 0.7228 (p0) REVERT: E 16 SER cc_start: 0.8362 (m) cc_final: 0.8133 (t) REVERT: E 158 SER cc_start: 0.8774 (t) cc_final: 0.8297 (p) REVERT: G 45 LYS cc_start: 0.7363 (mmtm) cc_final: 0.6970 (ptpp) REVERT: R 53 LYS cc_start: 0.7814 (mttt) cc_final: 0.7351 (mmtt) REVERT: R 74 VAL cc_start: 0.8005 (t) cc_final: 0.7693 (m) REVERT: R 129 MET cc_start: 0.8141 (mtp) cc_final: 0.7902 (mtp) REVERT: R 314 ASN cc_start: 0.7147 (t0) cc_final: 0.6878 (t0) outliers start: 25 outliers final: 22 residues processed: 143 average time/residue: 0.2573 time to fit residues: 51.2750 Evaluate side-chains 144 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 82 MET 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 85 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 81 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.175396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.134483 restraints weight = 10014.752| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.66 r_work: 0.3064 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.6208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10154 Z= 0.111 Angle : 0.479 6.801 13733 Z= 0.256 Chirality : 0.040 0.165 1550 Planarity : 0.004 0.049 1739 Dihedral : 4.901 89.654 1410 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.03 % Allowed : 15.12 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1248 helix: 2.76 (0.25), residues: 405 sheet: 0.22 (0.30), residues: 320 loop : -0.27 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 295 HIS 0.004 0.001 HIS A 197 PHE 0.013 0.001 PHE A 189 TYR 0.016 0.001 TYR E 190 ARG 0.007 0.000 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 468) hydrogen bonds : angle 4.08959 ( 1332) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.49007 ( 6) covalent geometry : bond 0.00253 (10151) covalent geometry : angle 0.47881 (13727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5852.36 seconds wall clock time: 103 minutes 24.79 seconds (6204.79 seconds total)