Starting phenix.real_space_refine on Thu Jul 2 09:42:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iod_35616/07_2026/8iod_35616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iod_35616/07_2026/8iod_35616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iod_35616/07_2026/8iod_35616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iod_35616/07_2026/8iod_35616.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8iod_35616/07_2026/8iod_35616.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iod_35616/07_2026/8iod_35616.cif" model { file = "/net/cci-nas-00/data/ceres_data/8iod_35616/07_2026/8iod_35616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iod_35616/07_2026/8iod_35616.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 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 Ca 1 9.91 5 S 67 5.16 5 C 5110 2.51 5 N 1401 2.21 5 O 1482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "L ASP 2": not complete - not flipped Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8061 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1943 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2567 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "G" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 405 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "L" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 74 Unusual residues: {'ACE': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="ACE L 0 " pdbres="NLE L 1 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 1, 'ASP:plan': 1, '4J2:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 946 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2124 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 5, 'TRANS': 264} Chain breaks: 1 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.20 Number of scatterers: 8061 At special positions: 0 Unit cell: (85.68, 93.177, 127.449, 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) Ca 1 19.99 S 67 16.00 O 1482 8.00 N 1401 7.00 C 5110 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 264 " - pdb=" SG CYS R 270 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 277.1 milliseconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 4J2 L 4 " Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 40.1% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.658A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.528A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.081A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.982A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 317 removed outlier: 3.524A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.744A pdb=" N ILE A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.747A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.574A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.898A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 43 Processing helix chain 'R' and resid 44 through 60 removed outlier: 3.530A pdb=" N GLU R 53 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 101 Processing helix chain 'R' and resid 107 through 146 Processing helix chain 'R' and resid 155 through 180 removed outlier: 4.399A pdb=" N ILE R 178 " --> pdb=" O GLY R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 220 removed outlier: 3.882A pdb=" N PHE R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU R 200 " --> pdb=" O ALA R 196 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG R 218 " --> pdb=" O THR R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 247 removed outlier: 3.637A pdb=" N PHE R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 261 Processing helix chain 'R' and resid 267 through 275 removed outlier: 3.583A pdb=" N PHE R 273 " --> pdb=" O TYR R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 296 removed outlier: 3.990A pdb=" N SER R 288 " --> pdb=" O ILE R 284 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL R 289 " --> pdb=" O MET R 285 " (cutoff:3.500A) Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 312 removed outlier: 3.627A pdb=" N CYS R 312 " --> pdb=" O GLU R 308 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 189 removed outlier: 6.226A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.314A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.390A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.089A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.226A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.838A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.763A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.552A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.776A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.904A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2028 1.33 - 1.45: 1651 1.45 - 1.57: 4443 1.57 - 1.69: 0 1.69 - 1.82: 99 Bond restraints: 8221 Sorted by residual: bond pdb=" CG ASP L 2 " pdb=" OD1 ASP L 2 " ideal model delta sigma weight residual 1.249 1.287 -0.038 1.90e-02 2.77e+03 4.00e+00 bond pdb=" CA 4J2 L 4 " pdb=" C 4J2 L 4 " ideal model delta sigma weight residual 1.525 1.559 -0.034 2.10e-02 2.27e+03 2.64e+00 bond pdb=" CG1 ILE R 178 " pdb=" CD1 ILE R 178 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.53e+00 bond pdb=" CG1 ILE R 144 " pdb=" CD1 ILE R 144 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.49e+00 bond pdb=" CB THR R 143 " pdb=" CG2 THR R 143 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.87e+00 ... (remaining 8216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.51: 11118 7.51 - 15.01: 2 15.01 - 22.52: 0 22.52 - 30.02: 0 30.02 - 37.53: 1 Bond angle restraints: 11121 Sorted by residual: angle pdb=" CB ASP L 2 " pdb=" CG ASP L 2 " pdb=" OD1 ASP L 2 " ideal model delta sigma weight residual 118.40 80.87 37.53 2.30e+00 1.89e-01 2.66e+02 angle pdb=" N ILE R 178 " pdb=" CA ILE R 178 " pdb=" C ILE R 178 " ideal model delta sigma weight residual 113.71 109.76 3.95 9.50e-01 1.11e+00 1.73e+01 angle pdb=" C ARG N 98 " pdb=" N CYS N 99 " pdb=" CA CYS N 99 " ideal model delta sigma weight residual 123.65 116.01 7.64 1.88e+00 2.83e-01 1.65e+01 angle pdb=" N TRP R 251 " pdb=" CA TRP R 251 " pdb=" C TRP R 251 " ideal model delta sigma weight residual 110.61 115.59 -4.98 1.25e+00 6.40e-01 1.59e+01 angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 122.23 116.01 6.22 1.57e+00 4.06e-01 1.57e+01 ... (remaining 11116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4398 17.52 - 35.05: 411 35.05 - 52.57: 70 52.57 - 70.09: 10 70.09 - 87.61: 8 Dihedral angle restraints: 4897 sinusoidal: 1921 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -8.62 -77.38 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CA TRP R 251 " pdb=" C TRP R 251 " pdb=" N ALA R 252 " pdb=" CA ALA R 252 " ideal model delta harmonic sigma weight residual 180.00 145.68 34.32 0 5.00e+00 4.00e-02 4.71e+01 dihedral pdb=" CA ASP L 2 " pdb=" CB ASP L 2 " pdb=" CG ASP L 2 " pdb=" OD1 ASP L 2 " ideal model delta sinusoidal sigma weight residual -30.00 -117.54 87.54 1 2.00e+01 2.50e-03 2.30e+01 ... (remaining 4894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 864 0.042 - 0.084: 295 0.084 - 0.127: 76 0.127 - 0.169: 17 0.169 - 0.211: 4 Chirality restraints: 1256 Sorted by residual: chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA TRP R 251 " pdb=" N TRP R 251 " pdb=" C TRP R 251 " pdb=" CB TRP R 251 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA ASN A 195 " pdb=" N ASN A 195 " pdb=" C ASN A 195 " pdb=" CB ASN A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.58e-01 ... (remaining 1253 not shown) Planarity restraints: 1410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 251 " 0.025 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP R 251 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP R 251 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP R 251 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 251 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 251 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 251 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 251 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 251 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP R 251 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " 0.052 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO G 60 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO B 194 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.031 5.00e-02 4.00e+02 ... (remaining 1407 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 96 2.61 - 3.18: 7171 3.18 - 3.76: 12962 3.76 - 4.33: 18198 4.33 - 4.90: 29533 Nonbonded interactions: 67960 Sorted by model distance: nonbonded pdb=" CG ASP L 2 " pdb=" NZ LYS L 7 " model vdw 2.038 3.350 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.047 3.040 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.183 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" O TYR B 85 " model vdw 2.208 3.120 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.221 3.040 ... (remaining 67955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.050 Find NCS groups from input model: 0.020 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:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 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 0.129 8226 Z= 0.272 Angle : 0.798 37.529 11127 Z= 0.445 Chirality : 0.047 0.211 1256 Planarity : 0.005 0.079 1410 Dihedral : 14.014 87.614 2962 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.83 (0.26), residues: 1001 helix: -0.08 (0.26), residues: 396 sheet: -0.53 (0.33), residues: 225 loop : -0.88 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 98 TYR 0.011 0.002 TYR A 278 PHE 0.024 0.002 PHE B 151 TRP 0.062 0.003 TRP R 251 HIS 0.017 0.002 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 ( 8221) covalent geometry : angle 0.79743 / 0.44 (11121) SS BOND : bond 0.00260 / 0.12 ( 3) SS BOND : angle 1.76333 / 0.53 ( 6) hydrogen bonds : bond 0.14709 / 9.38 ( 403) hydrogen bonds : angle 6.14164 / 4.26 ( 1152) Misc. bond : bond 0.11743 / 5.83 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.243 Fit side-chains REVERT: G 21 MET cc_start: 0.5680 (ptp) cc_final: 0.5129 (ptp) REVERT: G 44 HIS cc_start: 0.6793 (m-70) cc_final: 0.6557 (t-90) outliers start: 0 outliers final: 1 residues processed: 115 average time/residue: 0.3784 time to fit residues: 46.7080 Evaluate side-chains 93 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN A 231 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.218855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.177641 restraints weight = 7477.294| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.91 r_work: 0.3869 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8226 Z= 0.160 Angle : 0.603 7.197 11127 Z= 0.324 Chirality : 0.044 0.149 1256 Planarity : 0.005 0.071 1410 Dihedral : 5.162 37.246 1120 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.52 % Allowed : 7.78 % Favored : 89.70 % 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 (0.27), residues: 1001 helix: 0.61 (0.26), residues: 394 sheet: -0.36 (0.33), residues: 228 loop : -0.65 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.010 0.001 TYR R 72 PHE 0.017 0.002 PHE B 151 TRP 0.034 0.002 TRP R 251 HIS 0.012 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 8221) covalent geometry : angle 0.60188 / 0.32 (11121) SS BOND : bond 0.00323 / 0.16 ( 3) SS BOND : angle 1.78957 / 0.56 ( 6) hydrogen bonds : bond 0.04638 / 3.22 ( 403) hydrogen bonds : angle 4.95573 / 3.46 ( 1152) Misc. bond : bond 0.00009 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.215 Fit side-chains REVERT: A 256 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6710 (mp) REVERT: B 220 GLN cc_start: 0.6972 (mp10) cc_final: 0.6694 (mp10) REVERT: B 269 ILE cc_start: 0.7802 (pt) cc_final: 0.7055 (tp) REVERT: G 21 MET cc_start: 0.5231 (ptp) cc_final: 0.4796 (ptp) REVERT: G 44 HIS cc_start: 0.6772 (m-70) cc_final: 0.6126 (t-90) REVERT: R 83 MET cc_start: 0.6573 (tpp) cc_final: 0.5828 (ttp) REVERT: R 235 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6866 (tp-100) outliers start: 22 outliers final: 9 residues processed: 111 average time/residue: 0.3869 time to fit residues: 46.1119 Evaluate side-chains 105 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 235 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 0.0040 chunk 99 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN A 246 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.217208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.163112 restraints weight = 7430.104| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.20 r_work: 0.3870 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8226 Z= 0.178 Angle : 0.602 6.434 11127 Z= 0.323 Chirality : 0.044 0.159 1256 Planarity : 0.005 0.068 1410 Dihedral : 5.314 58.900 1120 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.86 % Allowed : 11.78 % Favored : 85.35 % 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: -0.15 (0.27), residues: 1001 helix: 0.77 (0.26), residues: 392 sheet: -0.41 (0.33), residues: 230 loop : -0.66 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.015 0.002 TYR B 59 PHE 0.020 0.002 PHE B 151 TRP 0.025 0.002 TRP R 251 HIS 0.011 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 8221) covalent geometry : angle 0.60101 / 0.32 (11121) SS BOND : bond 0.00368 / 0.18 ( 3) SS BOND : angle 1.77877 / 0.54 ( 6) hydrogen bonds : bond 0.04626 / 3.23 ( 403) hydrogen bonds : angle 4.82985 / 3.39 ( 1152) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.349 Fit side-chains REVERT: A 256 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6655 (mp) REVERT: B 173 THR cc_start: 0.5825 (t) cc_final: 0.5494 (t) REVERT: B 220 GLN cc_start: 0.7010 (mp10) cc_final: 0.6696 (mp10) REVERT: G 21 MET cc_start: 0.5434 (ptp) cc_final: 0.4800 (mtt) REVERT: G 44 HIS cc_start: 0.6753 (m-70) cc_final: 0.6277 (t-170) REVERT: N 117 TYR cc_start: 0.5286 (OUTLIER) cc_final: 0.3438 (p90) REVERT: R 83 MET cc_start: 0.6694 (tpp) cc_final: 0.5941 (ttp) REVERT: R 178 ILE cc_start: 0.6292 (OUTLIER) cc_final: 0.6050 (mt) REVERT: R 297 PHE cc_start: 0.6568 (m-80) cc_final: 0.6253 (m-80) outliers start: 25 outliers final: 12 residues processed: 112 average time/residue: 0.3615 time to fit residues: 43.6298 Evaluate side-chains 110 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 262 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 0.0670 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.218476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.162250 restraints weight = 7529.823| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.97 r_work: 0.3907 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8226 Z= 0.145 Angle : 0.556 5.774 11127 Z= 0.299 Chirality : 0.042 0.143 1256 Planarity : 0.004 0.062 1410 Dihedral : 4.859 28.898 1120 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.20 % Allowed : 13.50 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.27), residues: 1001 helix: 0.95 (0.26), residues: 394 sheet: -0.37 (0.34), residues: 228 loop : -0.60 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.011 0.001 TYR R 72 PHE 0.017 0.002 PHE B 151 TRP 0.021 0.002 TRP R 251 HIS 0.008 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 8221) covalent geometry : angle 0.55476 / 0.30 (11121) SS BOND : bond 0.00327 / 0.16 ( 3) SS BOND : angle 1.65846 / 0.50 ( 6) hydrogen bonds : bond 0.04189 / 2.94 ( 403) hydrogen bonds : angle 4.64314 / 3.26 ( 1152) Misc. bond : bond 0.00008 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.208 Fit side-chains REVERT: A 235 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.5294 (mm-30) REVERT: A 256 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6602 (mp) REVERT: B 96 ARG cc_start: 0.8170 (mtp180) cc_final: 0.7597 (mmp-170) REVERT: B 214 ARG cc_start: 0.6194 (mmp-170) cc_final: 0.5938 (mmp-170) REVERT: B 220 GLN cc_start: 0.6933 (mp10) cc_final: 0.5779 (tm-30) REVERT: G 21 MET cc_start: 0.5471 (ptp) cc_final: 0.4702 (mtt) REVERT: G 44 HIS cc_start: 0.6773 (m-70) cc_final: 0.6205 (t-170) REVERT: L 5 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8098 (mmt180) REVERT: N 117 TYR cc_start: 0.5334 (OUTLIER) cc_final: 0.3332 (p90) REVERT: R 43 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5478 (t80) REVERT: R 83 MET cc_start: 0.6780 (tpp) cc_final: 0.6039 (ttp) REVERT: R 178 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6037 (mt) REVERT: R 235 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6946 (tp-100) REVERT: R 285 MET cc_start: 0.7466 (ttm) cc_final: 0.7179 (mtp) REVERT: R 297 PHE cc_start: 0.6480 (m-80) cc_final: 0.6111 (m-80) outliers start: 28 outliers final: 12 residues processed: 116 average time/residue: 0.4618 time to fit residues: 57.3536 Evaluate side-chains 118 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain L residue 5 ARG Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 235 GLN Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 282 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN N 82 GLN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.219252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.176935 restraints weight = 7544.948| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 2.56 r_work: 0.3877 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8226 Z= 0.137 Angle : 0.543 5.735 11127 Z= 0.292 Chirality : 0.042 0.142 1256 Planarity : 0.004 0.056 1410 Dihedral : 4.716 25.030 1120 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.00 % Allowed : 15.56 % Favored : 80.43 % 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: 0.13 (0.27), residues: 1001 helix: 1.12 (0.26), residues: 394 sheet: -0.35 (0.34), residues: 227 loop : -0.62 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 298 TYR 0.012 0.001 TYR B 59 PHE 0.017 0.002 PHE A 199 TRP 0.018 0.002 TRP R 251 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8221) covalent geometry : angle 0.54185 / 0.29 (11121) SS BOND : bond 0.00302 / 0.15 ( 3) SS BOND : angle 1.59587 / 0.48 ( 6) hydrogen bonds : bond 0.04054 / 2.85 ( 403) hydrogen bonds : angle 4.54950 / 3.20 ( 1152) Misc. bond : bond 0.00023 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.5195 (mm-30) REVERT: A 256 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6590 (mp) REVERT: B 96 ARG cc_start: 0.8091 (mtp180) cc_final: 0.7542 (mmp-170) REVERT: B 220 GLN cc_start: 0.6877 (mp10) cc_final: 0.5838 (tm-30) REVERT: G 21 MET cc_start: 0.5531 (ptp) cc_final: 0.4788 (mtt) REVERT: G 44 HIS cc_start: 0.6789 (m-70) cc_final: 0.6273 (t-170) REVERT: N 117 TYR cc_start: 0.5324 (OUTLIER) cc_final: 0.3288 (p90) REVERT: R 43 PHE cc_start: 0.6137 (OUTLIER) cc_final: 0.5485 (t80) REVERT: R 83 MET cc_start: 0.6712 (tpp) cc_final: 0.5933 (ttp) REVERT: R 178 ILE cc_start: 0.6457 (OUTLIER) cc_final: 0.6095 (mt) REVERT: R 235 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6852 (tp-100) REVERT: R 285 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7144 (mtp) REVERT: R 297 PHE cc_start: 0.6461 (m-80) cc_final: 0.6209 (m-80) outliers start: 35 outliers final: 15 residues processed: 114 average time/residue: 0.3787 time to fit residues: 46.4023 Evaluate side-chains 112 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 235 GLN Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 285 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 25 optimal weight: 30.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN A 246 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.219091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.164491 restraints weight = 7429.598| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.17 r_work: 0.3906 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8226 Z= 0.143 Angle : 0.549 5.969 11127 Z= 0.296 Chirality : 0.042 0.163 1256 Planarity : 0.004 0.053 1410 Dihedral : 4.689 24.620 1120 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.32 % Allowed : 17.28 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.15 (0.27), residues: 1001 helix: 1.14 (0.26), residues: 394 sheet: -0.38 (0.33), residues: 229 loop : -0.57 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 209 TYR 0.012 0.001 TYR N 60 PHE 0.027 0.002 PHE A 199 TRP 0.016 0.002 TRP R 251 HIS 0.007 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 8221) covalent geometry : angle 0.54830 / 0.30 (11121) SS BOND : bond 0.00290 / 0.14 ( 3) SS BOND : angle 1.57594 / 0.47 ( 6) hydrogen bonds : bond 0.04059 / 2.86 ( 403) hydrogen bonds : angle 4.55603 / 3.20 ( 1152) Misc. bond : bond 0.00015 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.203 Fit side-chains REVERT: A 199 PHE cc_start: 0.6785 (m-80) cc_final: 0.6561 (m-80) REVERT: A 235 GLU cc_start: 0.5871 (OUTLIER) cc_final: 0.5298 (mm-30) REVERT: A 256 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6571 (mp) REVERT: B 96 ARG cc_start: 0.8205 (mtp180) cc_final: 0.7608 (mmp-170) REVERT: B 220 GLN cc_start: 0.6884 (mp10) cc_final: 0.5801 (tm-30) REVERT: G 21 MET cc_start: 0.5284 (ptp) cc_final: 0.4658 (mtt) REVERT: G 44 HIS cc_start: 0.6784 (m-70) cc_final: 0.6186 (t-170) REVERT: N 117 TYR cc_start: 0.5490 (OUTLIER) cc_final: 0.3229 (p90) REVERT: R 43 PHE cc_start: 0.6097 (OUTLIER) cc_final: 0.5425 (t80) REVERT: R 83 MET cc_start: 0.6845 (tpp) cc_final: 0.6048 (ttp) REVERT: R 178 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.5983 (mt) REVERT: R 235 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6908 (tp-100) REVERT: R 285 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7167 (mtp) REVERT: R 290 MET cc_start: 0.6228 (tpp) cc_final: 0.5800 (mmm) REVERT: R 297 PHE cc_start: 0.6423 (m-80) cc_final: 0.6125 (m-80) outliers start: 29 outliers final: 16 residues processed: 110 average time/residue: 0.3815 time to fit residues: 45.2929 Evaluate side-chains 114 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 235 GLN Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 285 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 30.0000 chunk 12 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.219883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.164168 restraints weight = 7501.205| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.95 r_work: 0.3931 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8226 Z= 0.134 Angle : 0.553 7.406 11127 Z= 0.297 Chirality : 0.042 0.152 1256 Planarity : 0.004 0.051 1410 Dihedral : 4.768 36.201 1120 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.20 % Allowed : 17.39 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.25 (0.27), residues: 1001 helix: 1.27 (0.26), residues: 394 sheet: -0.34 (0.33), residues: 228 loop : -0.57 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.013 0.001 TYR N 60 PHE 0.023 0.002 PHE A 199 TRP 0.017 0.002 TRP R 251 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8221) covalent geometry : angle 0.54506 / 0.29 (11121) SS BOND : bond 0.01075 / 0.51 ( 3) SS BOND : angle 4.09158 / 1.61 ( 6) hydrogen bonds : bond 0.03910 / 2.76 ( 403) hydrogen bonds : angle 4.49021 / 3.16 ( 1152) Misc. bond : bond 0.00004 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 235 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.4967 (mm-30) REVERT: A 256 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6578 (mp) REVERT: B 96 ARG cc_start: 0.8137 (mtp180) cc_final: 0.7605 (mmp-170) REVERT: B 218 CYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7401 (t) REVERT: G 21 MET cc_start: 0.4990 (ptp) cc_final: 0.4407 (mtt) REVERT: G 44 HIS cc_start: 0.6939 (m-70) cc_final: 0.6087 (t-170) REVERT: N 117 TYR cc_start: 0.5467 (OUTLIER) cc_final: 0.3216 (p90) REVERT: R 43 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.5421 (t80) REVERT: R 83 MET cc_start: 0.6850 (tpp) cc_final: 0.6062 (ttp) REVERT: R 178 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.5895 (mt) REVERT: R 235 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6911 (tp-100) REVERT: R 285 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7149 (mtp) REVERT: R 297 PHE cc_start: 0.6403 (m-80) cc_final: 0.6107 (m-80) outliers start: 28 outliers final: 14 residues processed: 110 average time/residue: 0.3594 time to fit residues: 42.6642 Evaluate side-chains 111 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 235 GLN Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 285 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.216963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.173348 restraints weight = 7492.211| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.86 r_work: 0.3885 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8226 Z= 0.188 Angle : 0.609 6.960 11127 Z= 0.327 Chirality : 0.044 0.179 1256 Planarity : 0.004 0.053 1410 Dihedral : 5.017 35.447 1120 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.20 % Allowed : 18.31 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.03 (0.27), residues: 1001 helix: 1.03 (0.26), residues: 392 sheet: -0.39 (0.34), residues: 229 loop : -0.66 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.016 0.002 TYR R 72 PHE 0.022 0.002 PHE B 151 TRP 0.015 0.002 TRP B 99 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 ( 8221) covalent geometry : angle 0.60455 / 0.33 (11121) SS BOND : bond 0.00878 / 0.42 ( 3) SS BOND : angle 3.35142 / 1.32 ( 6) hydrogen bonds : bond 0.04457 / 3.13 ( 403) hydrogen bonds : angle 4.67620 / 3.28 ( 1152) Misc. bond : bond 0.00003 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 235 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.5383 (mm-30) REVERT: A 256 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6587 (mp) REVERT: A 353 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6939 (tmm) REVERT: B 96 ARG cc_start: 0.8064 (mtp180) cc_final: 0.7629 (mmp-170) REVERT: B 220 GLN cc_start: 0.6829 (mp10) cc_final: 0.5792 (tm-30) REVERT: G 21 MET cc_start: 0.5130 (ptp) cc_final: 0.4467 (mtt) REVERT: N 117 TYR cc_start: 0.5272 (OUTLIER) cc_final: 0.2987 (p90) REVERT: R 43 PHE cc_start: 0.6241 (OUTLIER) cc_final: 0.5479 (t80) REVERT: R 83 MET cc_start: 0.6859 (tpp) cc_final: 0.6070 (ttp) REVERT: R 178 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6159 (mt) REVERT: R 235 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6206 (tt0) REVERT: R 285 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7150 (mtp) REVERT: R 297 PHE cc_start: 0.6546 (m-80) cc_final: 0.6288 (m-80) outliers start: 28 outliers final: 16 residues processed: 111 average time/residue: 0.3957 time to fit residues: 47.6110 Evaluate side-chains 115 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 235 GLN Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 285 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.219969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.175715 restraints weight = 7450.478| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.58 r_work: 0.3917 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8226 Z= 0.131 Angle : 0.553 7.035 11127 Z= 0.298 Chirality : 0.042 0.155 1256 Planarity : 0.004 0.052 1410 Dihedral : 4.760 34.377 1118 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.75 % Allowed : 19.57 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.24 (0.27), residues: 1001 helix: 1.29 (0.27), residues: 394 sheet: -0.35 (0.34), residues: 227 loop : -0.61 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 209 TYR 0.015 0.001 TYR R 72 PHE 0.018 0.002 PHE A 199 TRP 0.020 0.002 TRP R 251 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 8221) covalent geometry : angle 0.54946 / 0.30 (11121) SS BOND : bond 0.00726 / 0.35 ( 3) SS BOND : angle 2.82293 / 1.09 ( 6) hydrogen bonds : bond 0.03923 / 2.76 ( 403) hydrogen bonds : angle 4.51849 / 3.17 ( 1152) Misc. bond : bond 0.00001 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 235 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.4926 (mm-30) REVERT: A 256 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6552 (mp) REVERT: B 96 ARG cc_start: 0.8159 (mtp180) cc_final: 0.7553 (mmp-170) REVERT: G 21 MET cc_start: 0.5075 (ptp) cc_final: 0.4507 (mtt) REVERT: G 44 HIS cc_start: 0.6944 (m-70) cc_final: 0.6048 (t-170) REVERT: N 117 TYR cc_start: 0.5393 (OUTLIER) cc_final: 0.3136 (p90) REVERT: R 43 PHE cc_start: 0.6030 (OUTLIER) cc_final: 0.5369 (t80) REVERT: R 83 MET cc_start: 0.6841 (tpp) cc_final: 0.6052 (ttp) REVERT: R 178 ILE cc_start: 0.6357 (OUTLIER) cc_final: 0.5869 (mt) REVERT: R 235 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6919 (tp-100) REVERT: R 285 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7139 (mtp) REVERT: R 297 PHE cc_start: 0.6391 (m-80) cc_final: 0.6083 (m-80) outliers start: 24 outliers final: 12 residues processed: 106 average time/residue: 0.4490 time to fit residues: 51.3650 Evaluate side-chains 107 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 235 GLN Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 285 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.220611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.178351 restraints weight = 7446.269| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 2.39 r_work: 0.3920 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8226 Z= 0.127 Angle : 0.548 8.841 11127 Z= 0.295 Chirality : 0.042 0.165 1256 Planarity : 0.004 0.050 1410 Dihedral : 4.669 32.523 1118 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.52 % Allowed : 19.68 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.31 (0.27), residues: 1001 helix: 1.39 (0.27), residues: 392 sheet: -0.36 (0.33), residues: 228 loop : -0.58 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.016 0.001 TYR N 60 PHE 0.019 0.002 PHE A 199 TRP 0.019 0.002 TRP R 251 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8221) covalent geometry : angle 0.54495 / 0.29 (11121) SS BOND : bond 0.00626 / 0.30 ( 3) SS BOND : angle 2.65485 / 1.01 ( 6) hydrogen bonds : bond 0.03862 / 2.72 ( 403) hydrogen bonds : angle 4.47245 / 3.15 ( 1152) Misc. bond : bond 0.00006 / 0.00 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6573 (mp) REVERT: B 96 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7561 (mmp-170) REVERT: B 198 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.5917 (pp) REVERT: B 269 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6761 (tp) REVERT: G 21 MET cc_start: 0.5202 (ptp) cc_final: 0.4551 (mtt) REVERT: G 44 HIS cc_start: 0.6925 (m-70) cc_final: 0.6153 (t-170) REVERT: N 117 TYR cc_start: 0.5208 (OUTLIER) cc_final: 0.3024 (p90) REVERT: R 43 PHE cc_start: 0.6210 (OUTLIER) cc_final: 0.5561 (t80) REVERT: R 83 MET cc_start: 0.6743 (tpp) cc_final: 0.5998 (ttp) REVERT: R 178 ILE cc_start: 0.6232 (OUTLIER) cc_final: 0.5854 (mt) REVERT: R 235 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6846 (tp-100) REVERT: R 285 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7108 (mtp) REVERT: R 290 MET cc_start: 0.6287 (tpp) cc_final: 0.5839 (mmm) REVERT: R 297 PHE cc_start: 0.6496 (m-80) cc_final: 0.6224 (m-80) outliers start: 22 outliers final: 11 residues processed: 105 average time/residue: 0.4465 time to fit residues: 50.4172 Evaluate side-chains 110 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 43 PHE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 178 ILE Chi-restraints excluded: chain R residue 235 GLN Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 285 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 87 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 56 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 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 = 0.4677 r_free = 0.4677 target = 0.222840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.177389 restraints weight = 7461.001| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 2.59 r_work: 0.3917 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8226 Z= 0.112 Angle : 0.532 9.603 11127 Z= 0.286 Chirality : 0.041 0.162 1256 Planarity : 0.004 0.049 1410 Dihedral : 4.551 31.088 1118 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.06 % Allowed : 20.25 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.42 (0.27), residues: 1001 helix: 1.50 (0.27), residues: 395 sheet: -0.33 (0.33), residues: 227 loop : -0.54 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.016 0.001 TYR N 60 PHE 0.016 0.001 PHE A 199 TRP 0.019 0.002 TRP R 251 HIS 0.004 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 8221) covalent geometry : angle 0.52922 / 0.29 (11121) SS BOND : bond 0.00587 / 0.28 ( 3) SS BOND : angle 2.45289 / 0.93 ( 6) hydrogen bonds : bond 0.03670 / 2.58 ( 403) hydrogen bonds : angle 4.40951 / 3.10 ( 1152) Misc. bond : bond 0.00013 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5437.04 seconds wall clock time: 92 minutes 49.85 seconds (5569.85 seconds total)