Starting phenix.real_space_refine on Wed Feb 4 04:41:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wpm_66145/02_2026/9wpm_66145.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wpm_66145/02_2026/9wpm_66145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wpm_66145/02_2026/9wpm_66145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wpm_66145/02_2026/9wpm_66145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wpm_66145/02_2026/9wpm_66145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wpm_66145/02_2026/9wpm_66145.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5597 2.51 5 N 1478 2.21 5 O 1602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8731 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2110 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 2, 'ARG:plan': 4, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1586 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 11, 'GLU:plan': 13, 'GLN:plan1': 3, 'ASN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 155 Chain: "N" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 887 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2272 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 5, 'TRANS': 322} Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ARG:plan': 14, 'ASP:plan': 14, 'HIS:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 176 Chain: "Y" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 298 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 39} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1578 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain breaks: 3 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 5, 'GLU:plan': 8, 'ASP:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 96 Time building chain proxies: 1.83, per 1000 atoms: 0.21 Number of scatterers: 8731 At special positions: 0 Unit cell: (82, 119.72, 125.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1602 8.00 N 1478 7.00 C 5597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.06 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 332.3 milliseconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 16 sheets defined 33.1% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 23 through 51 removed outlier: 3.772A pdb=" N PHE A 27 " --> pdb=" O GLN A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 86 Proline residue: A 78 - end of helix removed outlier: 4.251A pdb=" N LEU A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 127 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 136 through 163 Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 193 through 227 removed outlier: 4.041A pdb=" N LEU A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 258 removed outlier: 3.557A pdb=" N ARG A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N MET A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.502A pdb=" N VAL A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 290 removed outlier: 3.771A pdb=" N MET A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'C' and resid 6 through 31 removed outlier: 4.156A pdb=" N VAL C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 210 through 216 removed outlier: 3.771A pdb=" N ASN C 216 " --> pdb=" O GLN C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 298 through 319 removed outlier: 3.640A pdb=" N ILE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER C 319 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 358 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.524A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.611A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.791A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 25 Processing helix chain 'Y' and resid 16 through 25 removed outlier: 3.766A pdb=" N ILE Y 25 " --> pdb=" O MET Y 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 191 removed outlier: 6.247A pdb=" N HIS C 34 " --> pdb=" O HIS C 197 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N PHE C 199 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C 220 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE C 221 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE C 257 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE C 223 " --> pdb=" O PHE C 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.519A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.097A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.798A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.794A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.754A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.697A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.782A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.568A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.342A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 8 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 11 removed outlier: 5.957A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 11 removed outlier: 5.957A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.541A pdb=" N THR S 213 " --> pdb=" O SER S 206 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.649A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 174 through 176 443 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.04 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: 1403 1.31 - 1.44: 2563 1.44 - 1.56: 4877 1.56 - 1.69: 1 1.69 - 1.82: 76 Bond restraints: 8920 Sorted by residual: bond pdb=" CA LEU B 308 " pdb=" C LEU B 308 " ideal model delta sigma weight residual 1.528 1.476 0.052 1.04e-02 9.25e+03 2.49e+01 bond pdb=" CA ASP A 19 " pdb=" C ASP A 19 " ideal model delta sigma weight residual 1.519 1.464 0.055 1.16e-02 7.43e+03 2.26e+01 bond pdb=" CA GLN A 99 " pdb=" C GLN A 99 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.30e-02 5.92e+03 1.86e+01 bond pdb=" CA LEU A 186 " pdb=" C LEU A 186 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.27e-02 6.20e+03 1.73e+01 bond pdb=" C ALA A 97 " pdb=" O ALA A 97 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.19e-02 7.06e+03 1.69e+01 ... (remaining 8915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 12041 3.47 - 6.94: 113 6.94 - 10.41: 34 10.41 - 13.87: 5 13.87 - 17.34: 2 Bond angle restraints: 12195 Sorted by residual: angle pdb=" N GLU A 21 " pdb=" CA GLU A 21 " pdb=" C GLU A 21 " ideal model delta sigma weight residual 109.96 92.62 17.34 1.50e+00 4.44e-01 1.34e+02 angle pdb=" N PRO A 20 " pdb=" CA PRO A 20 " pdb=" C PRO A 20 " ideal model delta sigma weight residual 114.35 100.78 13.57 1.25e+00 6.40e-01 1.18e+02 angle pdb=" N THR A 191 " pdb=" CA THR A 191 " pdb=" C THR A 191 " ideal model delta sigma weight residual 112.88 99.01 13.87 1.29e+00 6.01e-01 1.16e+02 angle pdb=" N ASP A 18 " pdb=" CA ASP A 18 " pdb=" C ASP A 18 " ideal model delta sigma weight residual 110.10 94.98 15.12 1.49e+00 4.50e-01 1.03e+02 angle pdb=" N THR A 278 " pdb=" CA THR A 278 " pdb=" C THR A 278 " ideal model delta sigma weight residual 111.14 120.74 -9.60 1.08e+00 8.57e-01 7.89e+01 ... (remaining 12190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4602 16.99 - 33.99: 411 33.99 - 50.98: 94 50.98 - 67.97: 13 67.97 - 84.96: 8 Dihedral angle restraints: 5128 sinusoidal: 1546 harmonic: 3582 Sorted by residual: dihedral pdb=" C ILE A 281 " pdb=" N ILE A 281 " pdb=" CA ILE A 281 " pdb=" CB ILE A 281 " ideal model delta harmonic sigma weight residual -122.00 -137.23 15.23 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" N ILE A 281 " pdb=" C ILE A 281 " pdb=" CA ILE A 281 " pdb=" CB ILE A 281 " ideal model delta harmonic sigma weight residual 123.40 135.03 -11.63 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" CA GLN A 269 " pdb=" C GLN A 269 " pdb=" N ASP A 270 " pdb=" CA ASP A 270 " ideal model delta harmonic sigma weight residual 180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 5125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1316 0.094 - 0.189: 105 0.189 - 0.283: 24 0.283 - 0.377: 5 0.377 - 0.471: 4 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CA PHE A 100 " pdb=" N PHE A 100 " pdb=" C PHE A 100 " pdb=" CB PHE A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" CA ASP A 19 " pdb=" N ASP A 19 " pdb=" C ASP A 19 " pdb=" CB ASP A 19 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA ILE A 281 " pdb=" N ILE A 281 " pdb=" C ILE A 281 " pdb=" CB ILE A 281 " both_signs ideal model delta sigma weight residual False 2.43 2.02 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 1451 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 175 " -0.019 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C HIS A 175 " 0.069 2.00e-02 2.50e+03 pdb=" O HIS A 175 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE A 176 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR Y 52 " -0.065 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO Y 53 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO Y 53 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO Y 53 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 77 " 0.063 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO A 78 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " 0.052 5.00e-02 4.00e+02 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 831 2.74 - 3.28: 8660 3.28 - 3.82: 15266 3.82 - 4.36: 17911 4.36 - 4.90: 31411 Nonbonded interactions: 74079 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.203 3.040 nonbonded pdb=" O ALA A 155 " pdb=" OG1 THR A 159 " model vdw 2.229 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR N 117 " pdb=" O CYS B 204 " model vdw 2.241 3.040 nonbonded pdb=" OG SER S 161 " pdb=" O LYS S 163 " model vdw 2.280 3.040 ... (remaining 74074 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: 4.050 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 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 : 0.006 0.105 8924 Z= 0.355 Angle : 0.944 17.343 12203 Z= 0.584 Chirality : 0.063 0.471 1454 Planarity : 0.007 0.095 1549 Dihedral : 14.442 84.963 2804 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.63 % Allowed : 24.75 % Favored : 74.62 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.24), residues: 1206 helix: 1.03 (0.27), residues: 362 sheet: -0.22 (0.30), residues: 291 loop : -0.79 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.023 0.002 TYR A 277 PHE 0.030 0.002 PHE A 103 TRP 0.016 0.002 TRP C 211 HIS 0.007 0.002 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 8920) covalent geometry : angle 0.94170 (12195) SS BOND : bond 0.01431 ( 4) SS BOND : angle 2.67146 ( 8) hydrogen bonds : bond 0.19711 ( 441) hydrogen bonds : angle 7.76786 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.199 Fit side-chains REVERT: A 103 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.6341 (t80) outliers start: 5 outliers final: 1 residues processed: 124 average time/residue: 0.4204 time to fit residues: 56.3458 Evaluate side-chains 111 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 103 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.0060 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 55 HIS A 127 ASN B 88 ASN B 125 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.135947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.124311 restraints weight = 13550.351| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.47 r_work: 0.3716 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8924 Z= 0.145 Angle : 0.583 7.971 12203 Z= 0.315 Chirality : 0.043 0.167 1454 Planarity : 0.006 0.059 1549 Dihedral : 5.059 45.342 1309 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.44 % Allowed : 19.92 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.24), residues: 1206 helix: 1.70 (0.27), residues: 362 sheet: -0.01 (0.31), residues: 296 loop : -0.66 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG S 72 TYR 0.039 0.002 TYR A 277 PHE 0.016 0.002 PHE A 250 TRP 0.020 0.002 TRP B 211 HIS 0.005 0.002 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8920) covalent geometry : angle 0.58254 (12195) SS BOND : bond 0.00282 ( 4) SS BOND : angle 1.18487 ( 8) hydrogen bonds : bond 0.04573 ( 441) hydrogen bonds : angle 5.44657 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.436 Fit side-chains REVERT: A 93 PHE cc_start: 0.5679 (OUTLIER) cc_final: 0.5347 (m-80) REVERT: A 164 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6608 (ttm170) REVERT: C 316 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7815 (t) REVERT: C 345 ASP cc_start: 0.7648 (m-30) cc_final: 0.7433 (m-30) REVERT: N 53 GLN cc_start: 0.7637 (mp10) cc_final: 0.7387 (mp10) REVERT: S 146 SER cc_start: 0.7103 (t) cc_final: 0.6623 (m) outliers start: 35 outliers final: 12 residues processed: 144 average time/residue: 0.3906 time to fit residues: 60.8391 Evaluate side-chains 123 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 113 optimal weight: 0.2980 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 127 ASN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.132407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.120731 restraints weight = 13534.897| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.46 r_work: 0.3673 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8924 Z= 0.187 Angle : 0.597 7.189 12203 Z= 0.323 Chirality : 0.044 0.173 1454 Planarity : 0.005 0.055 1549 Dihedral : 4.892 23.820 1306 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.08 % Allowed : 18.91 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1206 helix: 1.69 (0.27), residues: 364 sheet: -0.06 (0.29), residues: 302 loop : -0.66 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 31 TYR 0.022 0.002 TYR A 72 PHE 0.016 0.002 PHE B 151 TRP 0.018 0.002 TRP B 82 HIS 0.006 0.002 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8920) covalent geometry : angle 0.59632 (12195) SS BOND : bond 0.00190 ( 4) SS BOND : angle 1.22230 ( 8) hydrogen bonds : bond 0.04528 ( 441) hydrogen bonds : angle 5.27723 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.209 Fit side-chains REVERT: A 164 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6587 (ttm170) REVERT: C 316 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7915 (t) REVERT: N 53 GLN cc_start: 0.7637 (mp10) cc_final: 0.7336 (mp10) REVERT: Y 38 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7385 (mtm) outliers start: 40 outliers final: 22 residues processed: 144 average time/residue: 0.3763 time to fit residues: 58.7921 Evaluate side-chains 133 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain Y residue 38 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 231 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 109 optimal weight: 0.4980 chunk 44 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 127 ASN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.131443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.119347 restraints weight = 13643.331| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.57 r_work: 0.3649 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8924 Z= 0.181 Angle : 0.582 6.653 12203 Z= 0.314 Chirality : 0.044 0.172 1454 Planarity : 0.005 0.056 1549 Dihedral : 4.879 22.497 1306 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.95 % Allowed : 20.43 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.24), residues: 1206 helix: 1.68 (0.27), residues: 363 sheet: -0.04 (0.29), residues: 302 loop : -0.64 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.022 0.002 TYR A 72 PHE 0.016 0.002 PHE A 106 TRP 0.016 0.002 TRP B 82 HIS 0.006 0.002 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8920) covalent geometry : angle 0.58109 (12195) SS BOND : bond 0.00178 ( 4) SS BOND : angle 1.08451 ( 8) hydrogen bonds : bond 0.04348 ( 441) hydrogen bonds : angle 5.17326 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 164 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6579 (ttm170) REVERT: C 316 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7922 (t) REVERT: N 53 GLN cc_start: 0.7635 (mp10) cc_final: 0.7298 (mp10) REVERT: B 101 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.6963 (mpt) REVERT: Y 38 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7378 (mtm) outliers start: 39 outliers final: 28 residues processed: 147 average time/residue: 0.3925 time to fit residues: 62.6620 Evaluate side-chains 143 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain Y residue 38 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 231 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 29 optimal weight: 0.4980 chunk 65 optimal weight: 0.0030 chunk 45 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 85 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 127 ASN B 88 ASN B 293 ASN S 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.134302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.122688 restraints weight = 13642.886| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.48 r_work: 0.3703 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8924 Z= 0.118 Angle : 0.520 6.682 12203 Z= 0.280 Chirality : 0.041 0.156 1454 Planarity : 0.005 0.054 1549 Dihedral : 4.472 20.869 1306 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.57 % Allowed : 21.70 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.24), residues: 1206 helix: 2.17 (0.27), residues: 357 sheet: -0.10 (0.29), residues: 308 loop : -0.44 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 98 TYR 0.021 0.001 TYR A 72 PHE 0.015 0.001 PHE A 106 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8920) covalent geometry : angle 0.52000 (12195) SS BOND : bond 0.00166 ( 4) SS BOND : angle 0.72292 ( 8) hydrogen bonds : bond 0.03802 ( 441) hydrogen bonds : angle 4.85250 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.321 Fit side-chains REVERT: A 93 PHE cc_start: 0.5731 (OUTLIER) cc_final: 0.5447 (t80) REVERT: N 53 GLN cc_start: 0.7592 (mp10) cc_final: 0.7233 (mp10) REVERT: B 59 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.7331 (t80) REVERT: B 101 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.6716 (mpt) REVERT: Y 38 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7401 (mtm) outliers start: 36 outliers final: 22 residues processed: 147 average time/residue: 0.4054 time to fit residues: 64.7826 Evaluate side-chains 137 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain Y residue 38 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 231 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 33 optimal weight: 0.0070 chunk 112 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 97 optimal weight: 0.8980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 127 ASN B 88 ASN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.121601 restraints weight = 13666.187| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.47 r_work: 0.3682 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8924 Z= 0.142 Angle : 0.534 6.789 12203 Z= 0.288 Chirality : 0.042 0.218 1454 Planarity : 0.005 0.054 1549 Dihedral : 4.523 20.230 1306 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.95 % Allowed : 21.57 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1206 helix: 1.98 (0.27), residues: 364 sheet: -0.11 (0.29), residues: 308 loop : -0.51 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 98 TYR 0.022 0.002 TYR A 72 PHE 0.021 0.001 PHE A 106 TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8920) covalent geometry : angle 0.53339 (12195) SS BOND : bond 0.00159 ( 4) SS BOND : angle 0.88685 ( 8) hydrogen bonds : bond 0.03932 ( 441) hydrogen bonds : angle 4.86491 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: N 53 GLN cc_start: 0.7618 (mp10) cc_final: 0.7336 (mp10) REVERT: B 59 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.7325 (t80) REVERT: B 101 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.6765 (mpt) REVERT: Y 38 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7412 (mtm) outliers start: 39 outliers final: 29 residues processed: 146 average time/residue: 0.4038 time to fit residues: 64.3144 Evaluate side-chains 142 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain Y residue 38 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 36 optimal weight: 0.0970 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 127 ASN B 88 ASN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.131304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119143 restraints weight = 13682.911| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.58 r_work: 0.3648 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8924 Z= 0.177 Angle : 0.567 6.785 12203 Z= 0.306 Chirality : 0.043 0.218 1454 Planarity : 0.005 0.055 1549 Dihedral : 4.744 20.171 1306 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.20 % Allowed : 21.83 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1206 helix: 1.83 (0.27), residues: 362 sheet: -0.03 (0.29), residues: 304 loop : -0.62 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.022 0.002 TYR A 72 PHE 0.022 0.002 PHE A 106 TRP 0.013 0.002 TRP B 82 HIS 0.006 0.002 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8920) covalent geometry : angle 0.56662 (12195) SS BOND : bond 0.00192 ( 4) SS BOND : angle 1.01494 ( 8) hydrogen bonds : bond 0.04207 ( 441) hydrogen bonds : angle 5.03011 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.243 Fit side-chains REVERT: C 27 LYS cc_start: 0.8123 (tttm) cc_final: 0.7902 (tttm) REVERT: C 345 ASP cc_start: 0.7899 (m-30) cc_final: 0.7622 (m-30) REVERT: N 53 GLN cc_start: 0.7629 (mp10) cc_final: 0.7338 (mp10) REVERT: B 101 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.6924 (mpt) REVERT: Y 38 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7400 (mtm) outliers start: 41 outliers final: 29 residues processed: 149 average time/residue: 0.3743 time to fit residues: 60.7985 Evaluate side-chains 144 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain Y residue 38 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 26 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 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 55 HIS A 127 ASN B 88 ASN S 231 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.131559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.119340 restraints weight = 13563.382| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.58 r_work: 0.3648 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8924 Z= 0.168 Angle : 0.561 6.931 12203 Z= 0.303 Chirality : 0.043 0.207 1454 Planarity : 0.005 0.054 1549 Dihedral : 4.741 20.537 1306 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.82 % Allowed : 21.95 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1206 helix: 1.83 (0.27), residues: 362 sheet: -0.03 (0.29), residues: 302 loop : -0.63 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.031 0.002 TYR A 277 PHE 0.024 0.002 PHE A 106 TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8920) covalent geometry : angle 0.55936 (12195) SS BOND : bond 0.00192 ( 4) SS BOND : angle 1.52607 ( 8) hydrogen bonds : bond 0.04141 ( 441) hydrogen bonds : angle 5.07461 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8147 (tttm) cc_final: 0.7918 (tttm) REVERT: C 345 ASP cc_start: 0.7890 (m-30) cc_final: 0.7602 (m-30) REVERT: N 53 GLN cc_start: 0.7637 (mp10) cc_final: 0.7343 (mp10) REVERT: B 101 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.6917 (mpt) REVERT: Y 38 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7413 (mtm) outliers start: 38 outliers final: 32 residues processed: 147 average time/residue: 0.3695 time to fit residues: 58.9682 Evaluate side-chains 151 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 38 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 231 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 65 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.0070 chunk 105 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 127 ASN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.133336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.121576 restraints weight = 13591.349| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.49 r_work: 0.3682 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8924 Z= 0.124 Angle : 0.529 6.906 12203 Z= 0.285 Chirality : 0.042 0.203 1454 Planarity : 0.004 0.052 1549 Dihedral : 4.515 19.902 1306 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.31 % Allowed : 22.59 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1206 helix: 2.15 (0.27), residues: 357 sheet: -0.12 (0.29), residues: 306 loop : -0.47 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 98 TYR 0.033 0.002 TYR A 277 PHE 0.022 0.001 PHE A 106 TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8920) covalent geometry : angle 0.52853 (12195) SS BOND : bond 0.00215 ( 4) SS BOND : angle 1.27660 ( 8) hydrogen bonds : bond 0.03833 ( 441) hydrogen bonds : angle 4.92306 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 11 PHE cc_start: 0.7341 (m-80) cc_final: 0.7082 (m-80) REVERT: A 93 PHE cc_start: 0.5726 (OUTLIER) cc_final: 0.5469 (t80) REVERT: C 27 LYS cc_start: 0.8140 (tttm) cc_final: 0.7915 (tttm) REVERT: N 53 GLN cc_start: 0.7628 (mp10) cc_final: 0.7246 (mp10) REVERT: B 101 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.6732 (mpt) REVERT: Y 38 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7423 (mtm) outliers start: 34 outliers final: 28 residues processed: 147 average time/residue: 0.3826 time to fit residues: 61.2050 Evaluate side-chains 147 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 38 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 111 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 127 ASN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.131289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119387 restraints weight = 13579.494| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.51 r_work: 0.3647 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8924 Z= 0.181 Angle : 0.574 6.959 12203 Z= 0.310 Chirality : 0.044 0.234 1454 Planarity : 0.005 0.054 1549 Dihedral : 4.764 20.401 1306 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.19 % Allowed : 23.22 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1206 helix: 1.90 (0.27), residues: 362 sheet: -0.09 (0.29), residues: 302 loop : -0.61 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.030 0.002 TYR A 277 PHE 0.025 0.002 PHE A 106 TRP 0.013 0.002 TRP B 82 HIS 0.006 0.002 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8920) covalent geometry : angle 0.57280 (12195) SS BOND : bond 0.00182 ( 4) SS BOND : angle 1.46286 ( 8) hydrogen bonds : bond 0.04216 ( 441) hydrogen bonds : angle 5.09816 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: C 27 LYS cc_start: 0.8171 (tttm) cc_final: 0.7936 (tttm) REVERT: C 345 ASP cc_start: 0.7821 (m-30) cc_final: 0.7582 (m-30) REVERT: N 53 GLN cc_start: 0.7643 (mp10) cc_final: 0.7254 (mp10) REVERT: B 101 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.6932 (mpt) REVERT: Y 38 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7425 (mtm) outliers start: 33 outliers final: 29 residues processed: 141 average time/residue: 0.4059 time to fit residues: 62.1512 Evaluate side-chains 147 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 38 MET Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 5 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 127 ASN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.130118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.118338 restraints weight = 13617.144| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.47 r_work: 0.3636 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8924 Z= 0.212 Angle : 0.609 7.007 12203 Z= 0.330 Chirality : 0.045 0.231 1454 Planarity : 0.005 0.056 1549 Dihedral : 5.005 20.999 1306 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.31 % Allowed : 22.72 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.24), residues: 1206 helix: 1.71 (0.27), residues: 361 sheet: -0.24 (0.29), residues: 313 loop : -0.67 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.027 0.002 TYR A 277 PHE 0.025 0.002 PHE A 106 TRP 0.014 0.002 TRP B 332 HIS 0.007 0.002 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 8920) covalent geometry : angle 0.60747 (12195) SS BOND : bond 0.00202 ( 4) SS BOND : angle 1.66757 ( 8) hydrogen bonds : bond 0.04464 ( 441) hydrogen bonds : angle 5.26138 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2940.29 seconds wall clock time: 50 minutes 47.73 seconds (3047.73 seconds total)