Starting phenix.real_space_refine on Tue May 13 06:56:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ium_35726/05_2025/8ium_35726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ium_35726/05_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_35726/05_2025/8ium_35726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ium_35726/05_2025/8ium_35726.map" model { file = "/net/cci-nas-00/data/ceres_data/8ium_35726/05_2025/8ium_35726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ium_35726/05_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-5687/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: 6.29, per 1000 atoms: 0.63 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: 3.05 Conformation dependent library (CDL) restraints added in 1.3 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: 1.24 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: 3.19 Time building geometry restraints manager: 3.19 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: 0.930 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.330 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- 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 : 1.138 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: 0.2507 time to fit residues: 68.7959 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 : 1.030 ------------------------------------------------------------------------------- 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 = 9842.955| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.70 r_work: 0.3218 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 1.225 Fit side-chains revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8188 (mtpp) REVERT: A 308 LYS cc_start: 0.8016 (tptt) cc_final: 0.7673 (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: 0.6312 (t0) REVERT: E 16 SER cc_start: 0.8120 (m) cc_final: 0.7779 (t) REVERT: E 17 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7771 (ttm-80) REVERT: N 34 MET cc_start: 0.8246 (mmt) cc_final: 0.7951 (mmm) REVERT: R 74 VAL cc_start: 0.8218 (t) cc_final: 0.7912 (m) REVERT: R 155 MET cc_start: 0.7195 (ptp) cc_final: 0.6985 (ptt) outliers start: 21 outliers final: 12 residues processed: 174 average time/residue: 0.3082 time to fit residues: 69.2963 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 : 1.127 ------------------------------------------------------------------------------- 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: 0.9990 chunk 8 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 103 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.187023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147036 restraints weight = 9896.054| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.57 r_work: 0.3297 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10154 Z= 0.111 Angle : 0.484 7.985 13733 Z= 0.255 Chirality : 0.040 0.160 1550 Planarity : 0.004 0.069 1739 Dihedral : 4.551 44.118 1410 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.66 % Allowed : 11.24 % Favored : 87.10 % 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: 0.63 (0.24), residues: 1248 helix: 2.30 (0.26), residues: 404 sheet: -0.13 (0.28), residues: 328 loop : -0.69 (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 0.013 0.001 TYR A 36 ARG 0.004 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 468) hydrogen bonds : angle 4.13928 ( 1332) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.40859 ( 6) covalent geometry : bond 0.00248 (10151) covalent geometry : angle 0.48421 (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 148 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.062 Fit side-chains REVERT: A 193 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8274 (mtpp) REVERT: A 197 HIS cc_start: 0.7883 (m-70) cc_final: 0.7465 (m-70) REVERT: A 206 ASP cc_start: 0.7302 (p0) cc_final: 0.7060 (p0) REVERT: A 308 LYS cc_start: 0.8007 (tptt) cc_final: 0.7774 (ttpt) REVERT: A 351 MET cc_start: 0.8700 (ttm) cc_final: 0.8268 (ttp) REVERT: B 151 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8757 (tp) REVERT: B 219 ARG cc_start: 0.8155 (mpt-90) cc_final: 0.7624 (mmp-170) REVERT: E 16 SER cc_start: 0.7973 (m) cc_final: 0.7640 (t) REVERT: G 45 LYS cc_start: 0.7176 (mmtm) cc_final: 0.6848 (mtmm) REVERT: N 34 MET cc_start: 0.8219 (mmt) cc_final: 0.7960 (mmm) outliers start: 18 outliers final: 9 residues processed: 144 average time/residue: 0.2861 time to fit residues: 54.9458 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 : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 151 LEU 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 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=4.00 ------------------------------------------------------------------------------- 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: 3.9990 chunk 114 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 G 58 ASN ** R 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 250 GLN R 297 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.164999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119124 restraints weight = 10056.721| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.94 r_work: 0.2919 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10154 Z= 0.221 Angle : 0.608 8.573 13733 Z= 0.317 Chirality : 0.045 0.195 1550 Planarity : 0.004 0.068 1739 Dihedral : 5.132 39.800 1410 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.40 % Allowed : 12.53 % Favored : 85.07 % 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: 0.62 (0.24), residues: 1248 helix: 2.19 (0.26), residues: 399 sheet: -0.08 (0.28), residues: 326 loop : -0.62 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 295 HIS 0.011 0.002 HIS A 197 PHE 0.019 0.002 PHE A 189 TYR 0.031 0.002 TYR E 190 ARG 0.003 0.001 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 468) hydrogen bonds : angle 4.56511 ( 1332) SS BOND : bond 0.00400 ( 3) SS BOND : angle 0.70157 ( 6) covalent geometry : bond 0.00534 (10151) covalent geometry : angle 0.60781 (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 163 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 185 PHE cc_start: 0.8220 (m-80) cc_final: 0.7962 (m-10) REVERT: A 193 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8476 (mtmt) REVERT: A 308 LYS cc_start: 0.8364 (tptt) cc_final: 0.7830 (ttpt) REVERT: A 321 ARG cc_start: 0.8020 (ptp90) cc_final: 0.7698 (ptp90) REVERT: A 351 MET cc_start: 0.8882 (ttm) cc_final: 0.8473 (ttp) REVERT: B 219 ARG cc_start: 0.8069 (mpt-90) cc_final: 0.7759 (mpt-90) REVERT: B 223 CYS cc_start: 0.8656 (p) cc_final: 0.8310 (p) REVERT: B 248 THR cc_start: 0.8797 (p) cc_final: 0.8544 (p) REVERT: E 16 SER cc_start: 0.8502 (m) cc_final: 0.8122 (t) REVERT: E 158 SER cc_start: 0.8871 (t) cc_final: 0.8435 (p) REVERT: E 186 GLN cc_start: 0.8494 (tt0) cc_final: 0.8101 (tt0) REVERT: G 20 MET cc_start: 0.5998 (mpp) cc_final: 0.5560 (mpp) REVERT: G 45 LYS cc_start: 0.7446 (mmtm) cc_final: 0.7018 (ptpp) REVERT: N 59 SER cc_start: 0.5834 (m) cc_final: 0.5498 (p) REVERT: R 37 MET cc_start: 0.8613 (ttp) cc_final: 0.8395 (ttp) REVERT: R 74 VAL cc_start: 0.8166 (t) cc_final: 0.7769 (m) outliers start: 26 outliers final: 21 residues processed: 155 average time/residue: 0.2637 time to fit residues: 54.9542 Evaluate side-chains 154 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 45 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 183 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 139 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 71 SER Chi-restraints excluded: chain R residue 217 LEU 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: 0.4980 chunk 123 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 0.0570 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN E 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.171332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.126211 restraints weight = 9997.434| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.85 r_work: 0.3062 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10154 Z= 0.103 Angle : 0.479 8.235 13733 Z= 0.252 Chirality : 0.040 0.159 1550 Planarity : 0.004 0.057 1739 Dihedral : 4.858 68.811 1410 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.67 % Allowed : 13.46 % Favored : 83.87 % 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: 1.00 (0.24), residues: 1248 helix: 2.69 (0.26), residues: 400 sheet: 0.07 (0.29), residues: 320 loop : -0.52 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 295 HIS 0.008 0.001 HIS A 197 PHE 0.014 0.001 PHE A 189 TYR 0.016 0.001 TYR E 190 ARG 0.006 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 468) hydrogen bonds : angle 4.16250 ( 1332) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.32944 ( 6) covalent geometry : bond 0.00229 (10151) covalent geometry : angle 0.47936 (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 162 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.131 Fit side-chains REVERT: A 193 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8139 (mtpp) REVERT: A 197 HIS cc_start: 0.7504 (m-70) cc_final: 0.7155 (m-70) REVERT: A 308 LYS cc_start: 0.8384 (tptt) cc_final: 0.7950 (ttpt) REVERT: B 219 ARG cc_start: 0.8174 (mpt-90) cc_final: 0.7889 (mpt-90) REVERT: B 223 CYS cc_start: 0.8595 (p) cc_final: 0.8291 (p) REVERT: B 225 GLN cc_start: 0.8880 (mt0) cc_final: 0.8520 (mt0) REVERT: B 308 ASP cc_start: 0.7975 (m-30) cc_final: 0.7459 (p0) REVERT: E 16 SER cc_start: 0.8279 (m) cc_final: 0.7977 (t) REVERT: E 186 GLN cc_start: 0.8471 (tt0) cc_final: 0.8160 (tt0) REVERT: G 45 LYS cc_start: 0.7298 (mmtm) cc_final: 0.7094 (ptpp) REVERT: N 59 SER cc_start: 0.6050 (m) cc_final: 0.5768 (p) REVERT: R 74 VAL cc_start: 0.8182 (t) cc_final: 0.7911 (m) REVERT: R 129 MET cc_start: 0.8062 (mtp) cc_final: 0.7788 (mtp) outliers start: 29 outliers final: 19 residues processed: 153 average time/residue: 0.2507 time to fit residues: 52.4250 Evaluate side-chains 144 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 151 LEU 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 71 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 259 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 4 optimal weight: 0.0170 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN R 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.174659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130202 restraints weight = 10025.210| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.81 r_work: 0.3138 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5704 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 : 0.465 9.070 13733 Z= 0.245 Chirality : 0.040 0.164 1550 Planarity : 0.003 0.053 1739 Dihedral : 4.733 69.878 1410 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.30 % Allowed : 13.73 % Favored : 83.96 % 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: 1.18 (0.25), residues: 1248 helix: 2.87 (0.26), residues: 400 sheet: 0.05 (0.29), residues: 326 loop : -0.35 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 295 HIS 0.006 0.001 HIS A 197 PHE 0.013 0.001 PHE A 189 TYR 0.014 0.001 TYR E 190 ARG 0.005 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 468) hydrogen bonds : angle 4.03951 ( 1332) SS BOND : bond 0.00178 ( 3) SS BOND : angle 0.31944 ( 6) covalent geometry : bond 0.00218 (10151) covalent geometry : angle 0.46521 (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 157 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.106 Fit side-chains REVERT: A 197 HIS cc_start: 0.7505 (m-70) cc_final: 0.7208 (m-70) REVERT: A 308 LYS cc_start: 0.8311 (tptt) cc_final: 0.7881 (ttpt) REVERT: B 144 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7537 (pt) REVERT: B 219 ARG cc_start: 0.8208 (mpt-90) cc_final: 0.7887 (mpt-90) REVERT: B 223 CYS cc_start: 0.8570 (p) cc_final: 0.8294 (p) REVERT: B 225 GLN cc_start: 0.8852 (mt0) cc_final: 0.8548 (mt0) REVERT: B 308 ASP cc_start: 0.8071 (m-30) cc_final: 0.7506 (p0) REVERT: E 16 SER cc_start: 0.8259 (m) cc_final: 0.7999 (t) REVERT: E 186 GLN cc_start: 0.8474 (tt0) cc_final: 0.8162 (tt0) REVERT: G 20 MET cc_start: 0.5943 (mpp) cc_final: 0.5493 (mpp) REVERT: N 59 SER cc_start: 0.6031 (m) cc_final: 0.5798 (p) REVERT: R 74 VAL cc_start: 0.8132 (t) cc_final: 0.7862 (m) outliers start: 25 outliers final: 19 residues processed: 150 average time/residue: 0.2457 time to fit residues: 50.3953 Evaluate side-chains 144 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 144 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 201 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 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 71 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 79 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** R 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.164312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.121784 restraints weight = 10333.398| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.79 r_work: 0.2957 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 10154 Z= 0.317 Angle : 0.680 10.543 13733 Z= 0.355 Chirality : 0.048 0.211 1550 Planarity : 0.005 0.058 1739 Dihedral : 5.549 93.055 1410 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.95 % Allowed : 13.64 % Favored : 83.41 % 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: 0.70 (0.24), residues: 1248 helix: 2.20 (0.25), residues: 395 sheet: 0.02 (0.29), residues: 318 loop : -0.53 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 87 HIS 0.014 0.003 HIS A 197 PHE 0.022 0.002 PHE A 189 TYR 0.029 0.002 TYR E 190 ARG 0.004 0.001 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.05095 ( 468) hydrogen bonds : angle 4.72591 ( 1332) SS BOND : bond 0.00485 ( 3) SS BOND : angle 0.77218 ( 6) covalent geometry : bond 0.00779 (10151) covalent geometry : angle 0.67997 (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 171 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 307 ARG cc_start: 0.8323 (ttp80) cc_final: 0.8086 (ttp80) REVERT: A 308 LYS cc_start: 0.8427 (tptt) cc_final: 0.7858 (ttpt) REVERT: A 351 MET cc_start: 0.9014 (ttm) cc_final: 0.8574 (ttp) REVERT: B 210 ASP cc_start: 0.8893 (p0) cc_final: 0.8611 (p0) REVERT: B 223 CYS cc_start: 0.8650 (p) cc_final: 0.8296 (p) REVERT: B 225 GLN cc_start: 0.8939 (mt0) cc_final: 0.8609 (mt0) REVERT: B 248 THR cc_start: 0.8890 (p) cc_final: 0.8649 (p) REVERT: B 272 ASP cc_start: 0.8275 (m-30) cc_final: 0.8071 (m-30) REVERT: E 16 SER cc_start: 0.8719 (m) cc_final: 0.8449 (t) REVERT: E 17 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.7914 (ttm-80) REVERT: E 58 TYR cc_start: 0.8404 (m-10) cc_final: 0.8133 (m-10) REVERT: E 76 ASN cc_start: 0.8427 (m-40) cc_final: 0.8204 (m-40) REVERT: E 158 SER cc_start: 0.9022 (t) cc_final: 0.8600 (p) REVERT: N 59 SER cc_start: 0.6278 (m) cc_final: 0.5977 (p) REVERT: R 314 ASN cc_start: 0.7178 (t0) cc_final: 0.6912 (t0) outliers start: 32 outliers final: 28 residues processed: 162 average time/residue: 0.2297 time to fit residues: 51.6402 Evaluate side-chains 157 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 151 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 B residue 327 ASP 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 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 71 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 102 optimal weight: 6.9990 chunk 15 optimal weight: 0.3980 chunk 115 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN R 81 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.173877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132779 restraints weight = 10116.726| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.75 r_work: 0.3004 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.6306 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= 0.106 Angle : 0.491 9.455 13733 Z= 0.259 Chirality : 0.040 0.161 1550 Planarity : 0.004 0.052 1739 Dihedral : 5.001 88.418 1410 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.58 % Allowed : 14.38 % Favored : 83.04 % 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: 1.01 (0.24), residues: 1248 helix: 2.59 (0.26), residues: 404 sheet: 0.16 (0.29), residues: 315 loop : -0.49 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 295 HIS 0.004 0.001 HIS A 197 PHE 0.014 0.001 PHE A 189 TYR 0.016 0.001 TYR E 190 ARG 0.004 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 468) hydrogen bonds : angle 4.22764 ( 1332) SS BOND : bond 0.00136 ( 3) SS BOND : angle 0.50736 ( 6) covalent geometry : bond 0.00234 (10151) covalent geometry : angle 0.49097 (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 160 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.037 Fit side-chains REVERT: A 307 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7847 (ttp80) REVERT: A 308 LYS cc_start: 0.8205 (tptt) cc_final: 0.7664 (ttpt) REVERT: B 219 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7612 (mpp80) REVERT: B 223 CYS cc_start: 0.8551 (p) cc_final: 0.8326 (p) REVERT: B 225 GLN cc_start: 0.8845 (mt0) cc_final: 0.8584 (mt0) REVERT: B 308 ASP cc_start: 0.8171 (m-30) cc_final: 0.7415 (p0) REVERT: E 16 SER cc_start: 0.8421 (m) cc_final: 0.8176 (t) REVERT: E 17 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7776 (ttm-80) REVERT: E 58 TYR cc_start: 0.7960 (m-10) cc_final: 0.7652 (m-10) REVERT: E 158 SER cc_start: 0.8885 (t) cc_final: 0.8426 (p) REVERT: G 20 MET cc_start: 0.6415 (mpp) cc_final: 0.6087 (mpp) REVERT: N 59 SER cc_start: 0.6136 (m) cc_final: 0.5884 (p) REVERT: R 74 VAL cc_start: 0.8035 (t) cc_final: 0.7720 (m) REVERT: R 129 MET cc_start: 0.8091 (mtp) cc_final: 0.7867 (mtp) REVERT: R 314 ASN cc_start: 0.7122 (t0) cc_final: 0.6851 (t0) outliers start: 28 outliers final: 20 residues processed: 151 average time/residue: 0.2462 time to fit residues: 51.2855 Evaluate side-chains 147 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 105 VAL Chi-restraints excluded: chain B residue 151 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 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.164705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.119295 restraints weight = 10192.104| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.81 r_work: 0.3037 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10154 Z= 0.129 Angle : 0.509 9.409 13733 Z= 0.268 Chirality : 0.041 0.163 1550 Planarity : 0.004 0.051 1739 Dihedral : 5.057 91.228 1410 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.12 % Allowed : 15.21 % Favored : 82.67 % 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: 1.13 (0.24), residues: 1248 helix: 2.66 (0.25), residues: 404 sheet: 0.18 (0.30), residues: 326 loop : -0.39 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 295 HIS 0.004 0.001 HIS R 243 PHE 0.018 0.001 PHE A 189 TYR 0.019 0.001 TYR E 190 ARG 0.004 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 468) hydrogen bonds : angle 4.22307 ( 1332) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.57172 ( 6) covalent geometry : bond 0.00302 (10151) covalent geometry : angle 0.50907 (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 155 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 307 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7825 (ttp80) REVERT: A 308 LYS cc_start: 0.8300 (tptt) cc_final: 0.7794 (ttpt) REVERT: B 202 ARG cc_start: 0.7883 (mmt-90) cc_final: 0.7642 (mmt-90) REVERT: B 219 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7728 (mpp80) REVERT: B 225 GLN cc_start: 0.8827 (mt0) cc_final: 0.8571 (mt0) REVERT: B 272 ASP cc_start: 0.8070 (m-30) cc_final: 0.7853 (m-30) REVERT: B 308 ASP cc_start: 0.8092 (m-30) cc_final: 0.7375 (p0) REVERT: E 16 SER cc_start: 0.8445 (m) cc_final: 0.8211 (t) REVERT: E 17 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.8052 (ttm-80) REVERT: E 158 SER cc_start: 0.8825 (t) cc_final: 0.8373 (p) REVERT: N 59 SER cc_start: 0.6354 (m) cc_final: 0.6112 (p) REVERT: R 74 VAL cc_start: 0.8163 (t) cc_final: 0.7854 (m) REVERT: R 129 MET cc_start: 0.8028 (mtp) cc_final: 0.7776 (mtp) REVERT: R 314 ASN cc_start: 0.7243 (t0) cc_final: 0.7003 (t0) outliers start: 23 outliers final: 22 residues processed: 150 average time/residue: 0.2495 time to fit residues: 51.0024 Evaluate side-chains 151 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 105 VAL Chi-restraints excluded: chain B residue 151 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 B residue 327 ASP 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 96 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 28 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.172735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.131010 restraints weight = 10121.552| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.72 r_work: 0.3077 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.6372 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= 0.128 Angle : 0.509 9.477 13733 Z= 0.267 Chirality : 0.041 0.165 1550 Planarity : 0.004 0.050 1739 Dihedral : 5.110 93.413 1410 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.30 % Allowed : 15.02 % Favored : 82.67 % 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: 1.18 (0.25), residues: 1248 helix: 2.68 (0.25), residues: 404 sheet: 0.28 (0.30), residues: 320 loop : -0.39 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 295 HIS 0.006 0.001 HIS A 197 PHE 0.016 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 0.03591 ( 468) hydrogen bonds : angle 4.20198 ( 1332) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.57944 ( 6) covalent geometry : bond 0.00298 (10151) covalent geometry : angle 0.50885 (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 160 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7925 (ttp80) REVERT: A 308 LYS cc_start: 0.8346 (tptt) cc_final: 0.7790 (ttpt) REVERT: B 202 ARG cc_start: 0.7953 (mmt-90) cc_final: 0.7710 (mmt180) REVERT: B 219 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7690 (mpp80) REVERT: B 272 ASP cc_start: 0.8259 (m-30) cc_final: 0.8051 (m-30) REVERT: B 308 ASP cc_start: 0.8228 (m-30) cc_final: 0.7437 (p0) REVERT: E 16 SER cc_start: 0.8462 (m) cc_final: 0.8231 (t) REVERT: E 17 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7990 (ttm-80) REVERT: E 158 SER cc_start: 0.8842 (t) cc_final: 0.8380 (p) REVERT: R 53 LYS cc_start: 0.7940 (mttt) cc_final: 0.7508 (mmtt) REVERT: R 74 VAL cc_start: 0.8159 (t) cc_final: 0.7834 (m) REVERT: R 129 MET cc_start: 0.8175 (mtp) cc_final: 0.7920 (mtp) REVERT: R 314 ASN cc_start: 0.7209 (t0) cc_final: 0.6944 (t0) outliers start: 25 outliers final: 23 residues processed: 153 average time/residue: 0.2428 time to fit residues: 51.2664 Evaluate side-chains 155 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 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 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 151 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 B residue 327 ASP 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 96 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 318 LEU 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: 5.9990 chunk 60 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 56 optimal weight: 0.0670 chunk 65 optimal weight: 0.0470 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.175391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.134343 restraints weight = 10039.161| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.77 r_work: 0.3108 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10154 Z= 0.104 Angle : 0.489 9.649 13733 Z= 0.257 Chirality : 0.040 0.163 1550 Planarity : 0.004 0.049 1739 Dihedral : 5.020 91.713 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 : 1.94 % Allowed : 15.48 % Favored : 82.58 % 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: 1.28 (0.25), residues: 1248 helix: 2.82 (0.25), residues: 404 sheet: 0.29 (0.30), residues: 315 loop : -0.34 (0.27), residues: 529 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 0.016 0.001 PHE A 189 TYR 0.015 0.001 TYR E 190 ARG 0.007 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 468) hydrogen bonds : angle 4.11820 ( 1332) SS BOND : bond 0.00181 ( 3) SS BOND : angle 0.52469 ( 6) covalent geometry : bond 0.00230 (10151) covalent geometry : angle 0.48850 (13727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5450.57 seconds wall clock time: 95 minutes 18.36 seconds (5718.36 seconds total)