Starting phenix.real_space_refine on Sun Apr 5 06:11:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2s_63591/04_2026/9m2s_63591.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2s_63591/04_2026/9m2s_63591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m2s_63591/04_2026/9m2s_63591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2s_63591/04_2026/9m2s_63591.map" model { file = "/net/cci-nas-00/data/ceres_data/9m2s_63591/04_2026/9m2s_63591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2s_63591/04_2026/9m2s_63591.cif" } resolution = 2.78 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= 0.021 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 55 5.16 5 C 5372 2.51 5 N 1450 2.21 5 O 1575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8452 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2516 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 304} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "A" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1926 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'N2P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.75, per 1000 atoms: 0.21 Number of scatterers: 8452 At special positions: 0 Unit cell: (81.396, 100.674, 140.301, 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 55 16.00 O 1575 8.00 N 1450 7.00 C 5372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 97 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 190 " distance=2.03 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 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: 0.81 Conformation dependent library (CDL) restraints added in 322.7 milliseconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 42.0% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'R' and resid 30 through 60 Processing helix chain 'R' and resid 65 through 95 removed outlier: 4.073A pdb=" N MET R 86 " --> pdb=" O GLY R 82 " (cutoff:3.500A) Proline residue: R 87 - end of helix removed outlier: 4.296A pdb=" N ILE R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 136 removed outlier: 3.942A pdb=" N PHE R 104 " --> pdb=" O TYR R 100 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER R 117 " --> pdb=" O LEU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 169 Processing helix chain 'R' and resid 178 through 184 Processing helix chain 'R' and resid 195 through 207 removed outlier: 3.540A pdb=" N VAL R 200 " --> pdb=" O ALA R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 235 removed outlier: 4.028A pdb=" N VAL R 215 " --> pdb=" O CYS R 211 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE R 221 " --> pdb=" O LEU R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 279 removed outlier: 4.022A pdb=" N VAL R 261 " --> pdb=" O THR R 257 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL R 262 " --> pdb=" O LEU R 258 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 280 through 283 removed outlier: 3.827A pdb=" N ASN R 283 " --> pdb=" O PRO R 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 280 through 283' Processing helix chain 'R' and resid 287 through 310 removed outlier: 3.599A pdb=" N ASN R 301 " --> pdb=" O LEU R 297 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER R 302 " --> pdb=" O GLY R 298 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 326 Processing helix chain 'R' and resid 327 through 330 Processing helix chain 'R' and resid 332 through 336 removed outlier: 3.755A pdb=" N ASP R 335 " --> pdb=" O ASN R 332 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE R 336 " --> pdb=" O SER R 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 332 through 336' Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.699A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'A' and resid 12 through 36 removed outlier: 3.843A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.856A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.795A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.674A pdb=" N ALA A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.750A pdb=" N ALA A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 205 removed outlier: 4.074A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.554A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.676A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.733A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.748A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.592A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.766A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.756A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.532A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.594A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 69 through 75 removed outlier: 5.002A pdb=" N VAL A 86 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1200 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: 1.38 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: 1.21 - 1.33: 2025 1.33 - 1.45: 1823 1.45 - 1.57: 4709 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 8635 Sorted by residual: bond pdb=" N VAL R 29 " pdb=" CA VAL R 29 " ideal model delta sigma weight residual 1.458 1.492 -0.034 9.00e-03 1.23e+04 1.45e+01 bond pdb=" N LEU N 79 " pdb=" CA LEU N 79 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.21e-02 6.83e+03 1.20e+01 bond pdb=" N VAL R 34 " pdb=" CA VAL R 34 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.17e-02 7.31e+03 1.18e+01 bond pdb=" C VAL R 34 " pdb=" O VAL R 34 " ideal model delta sigma weight residual 1.237 1.276 -0.039 1.13e-02 7.83e+03 1.18e+01 bond pdb=" N ILE R 38 " pdb=" CA ILE R 38 " ideal model delta sigma weight residual 1.461 1.502 -0.041 1.24e-02 6.50e+03 1.11e+01 ... (remaining 8630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 11044 1.17 - 2.34: 455 2.34 - 3.51: 164 3.51 - 4.68: 38 4.68 - 5.84: 12 Bond angle restraints: 11713 Sorted by residual: angle pdb=" CA GLY B 41 " pdb=" C GLY B 41 " pdb=" O GLY B 41 " ideal model delta sigma weight residual 122.23 117.99 4.24 6.90e-01 2.10e+00 3.78e+01 angle pdb=" N ASP B 312 " pdb=" CA ASP B 312 " pdb=" C ASP B 312 " ideal model delta sigma weight residual 113.28 107.44 5.84 1.22e+00 6.72e-01 2.29e+01 angle pdb=" N THR R 31 " pdb=" CA THR R 31 " pdb=" C THR R 31 " ideal model delta sigma weight residual 111.33 106.10 5.23 1.21e+00 6.83e-01 1.87e+01 angle pdb=" CA THR R 116 " pdb=" C THR R 116 " pdb=" O THR R 116 " ideal model delta sigma weight residual 120.55 116.09 4.46 1.06e+00 8.90e-01 1.77e+01 angle pdb=" N TYR R 36 " pdb=" CA TYR R 36 " pdb=" C TYR R 36 " ideal model delta sigma weight residual 111.71 106.99 4.72 1.15e+00 7.56e-01 1.68e+01 ... (remaining 11708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.86: 4604 15.86 - 31.72: 403 31.72 - 47.58: 85 47.58 - 63.44: 22 63.44 - 79.30: 7 Dihedral angle restraints: 5121 sinusoidal: 1993 harmonic: 3128 Sorted by residual: dihedral pdb=" CB CYS R 22 " pdb=" SG CYS R 22 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual -86.00 -136.07 50.07 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CA CYS R 22 " pdb=" CB CYS R 22 " pdb=" SG CYS R 22 " pdb=" SG CYS R 186 " ideal model delta sinusoidal sigma weight residual 79.00 4.64 74.36 1 2.00e+01 2.50e-03 1.75e+01 dihedral pdb=" CB LYS N 87 " pdb=" CG LYS N 87 " pdb=" CD LYS N 87 " pdb=" CE LYS N 87 " ideal model delta sinusoidal sigma weight residual 180.00 127.08 52.92 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 5118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1022 0.051 - 0.102: 228 0.102 - 0.153: 56 0.153 - 0.203: 15 0.203 - 0.254: 2 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA THR N 122 " pdb=" N THR N 122 " pdb=" C THR N 122 " pdb=" CB THR N 122 " both_signs ideal model delta sigma weight residual False 2.53 2.78 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASP R 202 " pdb=" N ASP R 202 " pdb=" C ASP R 202 " pdb=" CB ASP R 202 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA MET R 187 " pdb=" N MET R 187 " pdb=" C MET R 187 " pdb=" CB MET R 187 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1320 not shown) Planarity restraints: 1492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 90 " 0.218 9.50e-02 1.11e+02 9.76e-02 5.85e+00 pdb=" NE ARG A 90 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 90 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 90 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 90 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 62 " -0.199 9.50e-02 1.11e+02 8.93e-02 4.90e+00 pdb=" NE ARG C 62 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 62 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 62 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 62 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 236 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.022 5.00e-02 4.00e+02 ... (remaining 1489 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 995 2.75 - 3.29: 8218 3.29 - 3.83: 14252 3.83 - 4.36: 17081 4.36 - 4.90: 29812 Nonbonded interactions: 70358 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.216 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.223 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.274 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.292 3.040 ... (remaining 70353 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: 1.130 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.030 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.004 0.043 8640 Z= 0.266 Angle : 0.628 5.845 11723 Z= 0.418 Chirality : 0.049 0.254 1323 Planarity : 0.005 0.098 1492 Dihedral : 12.968 79.296 3086 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 0.55 (0.27), residues: 1061 helix: 1.89 (0.27), residues: 423 sheet: -0.58 (0.34), residues: 216 loop : -0.63 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.009 0.001 TYR R 288 PHE 0.012 0.001 PHE R 114 TRP 0.013 0.001 TRP A 96 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8635) covalent geometry : angle 0.62810 (11713) SS BOND : bond 0.00182 ( 5) SS BOND : angle 0.72508 ( 10) hydrogen bonds : bond 0.17158 ( 423) hydrogen bonds : angle 6.69833 ( 1200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.347 Fit side-chains REVERT: R 88 PHE cc_start: 0.7731 (m-80) cc_final: 0.7498 (m-80) REVERT: R 148 VAL cc_start: 0.7636 (t) cc_final: 0.7394 (p) REVERT: R 309 TYR cc_start: 0.7604 (m-80) cc_final: 0.7356 (m-80) REVERT: B 78 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7819 (mmtt) REVERT: B 212 ASP cc_start: 0.7124 (t0) cc_final: 0.6714 (t0) REVERT: B 217 MET cc_start: 0.6505 (ptt) cc_final: 0.6055 (ptt) REVERT: B 258 ASP cc_start: 0.6862 (t70) cc_final: 0.6238 (t0) REVERT: N 4 LEU cc_start: 0.8504 (mt) cc_final: 0.8293 (mp) REVERT: N 79 LEU cc_start: 0.8191 (tp) cc_final: 0.7653 (tp) REVERT: A 26 ASP cc_start: 0.7083 (m-30) cc_final: 0.6724 (m-30) REVERT: A 27 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7618 (ttpt) REVERT: A 73 LYS cc_start: 0.8206 (ptpp) cc_final: 0.7561 (ptpp) REVERT: A 166 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7077 (mm-30) REVERT: A 195 ASP cc_start: 0.7385 (m-30) cc_final: 0.7111 (m-30) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.5810 time to fit residues: 122.3396 Evaluate side-chains 179 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN R 132 GLN B 110 ASN B 230 ASN B 239 ASN C 18 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.116026 restraints weight = 11841.278| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.85 r_work: 0.3432 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8640 Z= 0.251 Angle : 0.607 8.287 11723 Z= 0.326 Chirality : 0.046 0.153 1323 Planarity : 0.004 0.039 1492 Dihedral : 4.547 33.123 1174 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.29 % Allowed : 11.00 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.55 (0.27), residues: 1061 helix: 1.88 (0.26), residues: 425 sheet: -0.53 (0.33), residues: 225 loop : -0.68 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.018 0.002 TYR A 191 PHE 0.014 0.002 PHE R 291 TRP 0.017 0.002 TRP A 133 HIS 0.012 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00590 ( 8635) covalent geometry : angle 0.60288 (11713) SS BOND : bond 0.00450 ( 5) SS BOND : angle 2.58610 ( 10) hydrogen bonds : bond 0.05147 ( 423) hydrogen bonds : angle 5.08877 ( 1200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.307 Fit side-chains REVERT: R 53 VAL cc_start: 0.8472 (t) cc_final: 0.8117 (m) REVERT: R 61 LYS cc_start: 0.7820 (mtpp) cc_final: 0.7583 (mtpp) REVERT: R 86 MET cc_start: 0.8110 (mtt) cc_final: 0.7801 (mtt) REVERT: R 309 TYR cc_start: 0.8181 (m-80) cc_final: 0.7885 (m-80) REVERT: B 75 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7869 (mt0) REVERT: B 186 ASP cc_start: 0.7787 (m-30) cc_final: 0.7476 (m-30) REVERT: B 212 ASP cc_start: 0.7683 (t0) cc_final: 0.7245 (t0) REVERT: B 258 ASP cc_start: 0.7369 (t70) cc_final: 0.7157 (t70) REVERT: N 32 TYR cc_start: 0.8538 (m-80) cc_final: 0.8254 (m-80) REVERT: N 79 LEU cc_start: 0.8141 (tp) cc_final: 0.7934 (tt) REVERT: A 26 ASP cc_start: 0.7679 (m-30) cc_final: 0.7406 (m-30) REVERT: A 27 LYS cc_start: 0.8393 (ttpt) cc_final: 0.8159 (ttpt) REVERT: A 166 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 195 ASP cc_start: 0.8029 (m-30) cc_final: 0.7725 (m-30) REVERT: A 201 SER cc_start: 0.8498 (t) cc_final: 0.8207 (p) outliers start: 21 outliers final: 9 residues processed: 198 average time/residue: 0.5376 time to fit residues: 113.7624 Evaluate side-chains 185 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 161 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 17 optimal weight: 0.0270 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 overall best weight: 0.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN R 275 ASN B 35 ASN B 340 ASN A 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.119359 restraints weight = 11665.506| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.86 r_work: 0.3486 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8640 Z= 0.103 Angle : 0.494 9.401 11723 Z= 0.261 Chirality : 0.041 0.144 1323 Planarity : 0.004 0.040 1492 Dihedral : 4.022 21.856 1174 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.29 % Allowed : 14.49 % Favored : 83.22 % 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: 0.95 (0.27), residues: 1061 helix: 2.41 (0.27), residues: 420 sheet: -0.45 (0.34), residues: 223 loop : -0.57 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.008 0.001 TYR N 80 PHE 0.012 0.001 PHE R 114 TRP 0.012 0.001 TRP A 96 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8635) covalent geometry : angle 0.49284 (11713) SS BOND : bond 0.00289 ( 5) SS BOND : angle 1.35655 ( 10) hydrogen bonds : bond 0.03744 ( 423) hydrogen bonds : angle 4.64058 ( 1200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.331 Fit side-chains REVERT: R 86 MET cc_start: 0.8137 (mtt) cc_final: 0.7769 (mtt) REVERT: R 309 TYR cc_start: 0.8042 (m-80) cc_final: 0.7760 (m-80) REVERT: B 52 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7877 (ptp90) REVERT: B 212 ASP cc_start: 0.7685 (t0) cc_final: 0.7272 (t0) REVERT: N 32 TYR cc_start: 0.8462 (m-80) cc_final: 0.8191 (m-80) REVERT: A 20 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: A 26 ASP cc_start: 0.7578 (m-30) cc_final: 0.7275 (m-30) REVERT: A 27 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8209 (ttpt) REVERT: A 166 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7451 (mm-30) REVERT: A 201 SER cc_start: 0.8477 (t) cc_final: 0.8197 (p) outliers start: 21 outliers final: 6 residues processed: 185 average time/residue: 0.5593 time to fit residues: 110.2752 Evaluate side-chains 185 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 161 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN B 35 ASN B 125 ASN B 340 ASN A 82 HIS A 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.132557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117952 restraints weight = 11684.375| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.85 r_work: 0.3465 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8640 Z= 0.154 Angle : 0.513 10.313 11723 Z= 0.272 Chirality : 0.043 0.161 1323 Planarity : 0.004 0.041 1492 Dihedral : 4.165 26.438 1174 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.51 % Allowed : 15.80 % Favored : 81.70 % 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: 0.96 (0.27), residues: 1061 helix: 2.37 (0.27), residues: 421 sheet: -0.46 (0.33), residues: 225 loop : -0.48 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.013 0.001 TYR A 191 PHE 0.012 0.001 PHE R 114 TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8635) covalent geometry : angle 0.51201 (11713) SS BOND : bond 0.00344 ( 5) SS BOND : angle 1.27268 ( 10) hydrogen bonds : bond 0.04049 ( 423) hydrogen bonds : angle 4.65584 ( 1200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.248 Fit side-chains REVERT: R 86 MET cc_start: 0.8186 (mtt) cc_final: 0.7859 (mtt) REVERT: B 19 ARG cc_start: 0.8443 (ttp80) cc_final: 0.7887 (ttp80) REVERT: B 22 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7801 (mtt180) REVERT: B 52 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7922 (ptp90) REVERT: B 186 ASP cc_start: 0.7764 (m-30) cc_final: 0.7438 (m-30) REVERT: B 212 ASP cc_start: 0.7705 (t0) cc_final: 0.7300 (t0) REVERT: B 279 SER cc_start: 0.7220 (p) cc_final: 0.6927 (m) REVERT: N 32 TYR cc_start: 0.8506 (m-80) cc_final: 0.8267 (m-80) REVERT: N 53 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7571 (mt0) REVERT: N 79 LEU cc_start: 0.8089 (tp) cc_final: 0.7889 (tt) REVERT: A 20 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: A 26 ASP cc_start: 0.7586 (m-30) cc_final: 0.7308 (m-30) REVERT: A 27 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8208 (ttpt) REVERT: A 95 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8052 (mptp) REVERT: A 166 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 195 ASP cc_start: 0.7909 (m-30) cc_final: 0.7605 (m-30) REVERT: A 201 SER cc_start: 0.8473 (t) cc_final: 0.8232 (p) outliers start: 23 outliers final: 11 residues processed: 193 average time/residue: 0.5727 time to fit residues: 117.1951 Evaluate side-chains 189 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 161 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 17 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 34 optimal weight: 0.0020 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN R 132 GLN B 35 ASN B 340 ASN A 82 HIS A 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.131118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.116488 restraints weight = 11588.370| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.85 r_work: 0.3440 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8640 Z= 0.219 Angle : 0.568 9.154 11723 Z= 0.300 Chirality : 0.045 0.164 1323 Planarity : 0.004 0.042 1492 Dihedral : 4.511 34.608 1174 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.16 % Allowed : 16.12 % Favored : 80.72 % 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: 0.80 (0.26), residues: 1061 helix: 2.18 (0.26), residues: 420 sheet: -0.52 (0.33), residues: 222 loop : -0.53 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 283 TYR 0.019 0.002 TYR R 309 PHE 0.014 0.002 PHE B 151 TRP 0.017 0.002 TRP B 82 HIS 0.008 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 8635) covalent geometry : angle 0.56615 (11713) SS BOND : bond 0.00439 ( 5) SS BOND : angle 1.47083 ( 10) hydrogen bonds : bond 0.04576 ( 423) hydrogen bonds : angle 4.82125 ( 1200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: R 61 LYS cc_start: 0.7880 (mtpp) cc_final: 0.7669 (mtpp) REVERT: R 86 MET cc_start: 0.8209 (mtt) cc_final: 0.7897 (mtt) REVERT: R 94 VAL cc_start: 0.8236 (t) cc_final: 0.7990 (p) REVERT: B 212 ASP cc_start: 0.7756 (t0) cc_final: 0.7303 (t0) REVERT: B 279 SER cc_start: 0.7292 (p) cc_final: 0.7045 (m) REVERT: N 32 TYR cc_start: 0.8555 (m-80) cc_final: 0.8307 (m-80) REVERT: N 53 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: A 20 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: A 26 ASP cc_start: 0.7600 (m-30) cc_final: 0.7323 (m-30) REVERT: A 27 LYS cc_start: 0.8441 (ttpt) cc_final: 0.8199 (ttpt) REVERT: A 95 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8022 (mptp) REVERT: A 166 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7459 (mm-30) REVERT: A 171 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8121 (m) REVERT: A 195 ASP cc_start: 0.7983 (m-30) cc_final: 0.7662 (m-30) REVERT: A 201 SER cc_start: 0.8466 (t) cc_final: 0.8247 (p) outliers start: 29 outliers final: 15 residues processed: 195 average time/residue: 0.4997 time to fit residues: 104.5310 Evaluate side-chains 193 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 171 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 81 optimal weight: 0.0870 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN B 340 ASN A 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.132725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118127 restraints weight = 11414.668| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.84 r_work: 0.3465 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8640 Z= 0.135 Angle : 0.520 8.673 11723 Z= 0.275 Chirality : 0.042 0.162 1323 Planarity : 0.004 0.042 1492 Dihedral : 4.287 26.841 1174 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.05 % Allowed : 17.76 % Favored : 79.19 % 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: 0.90 (0.26), residues: 1061 helix: 2.29 (0.26), residues: 421 sheet: -0.44 (0.34), residues: 214 loop : -0.53 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 232 TYR 0.014 0.001 TYR R 309 PHE 0.012 0.001 PHE B 199 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8635) covalent geometry : angle 0.51939 (11713) SS BOND : bond 0.00336 ( 5) SS BOND : angle 1.20458 ( 10) hydrogen bonds : bond 0.03957 ( 423) hydrogen bonds : angle 4.66584 ( 1200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: R 61 LYS cc_start: 0.7858 (mtpp) cc_final: 0.7645 (mtpp) REVERT: R 86 MET cc_start: 0.8142 (mtt) cc_final: 0.7797 (mtt) REVERT: R 94 VAL cc_start: 0.8264 (t) cc_final: 0.8007 (p) REVERT: R 292 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: B 212 ASP cc_start: 0.7691 (t0) cc_final: 0.7283 (t0) REVERT: N 32 TYR cc_start: 0.8551 (m-80) cc_final: 0.8264 (m-80) REVERT: A 16 LYS cc_start: 0.8015 (mttt) cc_final: 0.7291 (mttt) REVERT: A 20 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: A 26 ASP cc_start: 0.7581 (m-30) cc_final: 0.7296 (m-30) REVERT: A 27 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8221 (ttpt) REVERT: A 95 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8060 (mptp) REVERT: A 166 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7420 (mm-30) REVERT: A 171 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8077 (m) REVERT: A 195 ASP cc_start: 0.7916 (m-30) cc_final: 0.7602 (m-30) REVERT: A 201 SER cc_start: 0.8442 (t) cc_final: 0.8222 (p) outliers start: 28 outliers final: 15 residues processed: 194 average time/residue: 0.5477 time to fit residues: 113.4616 Evaluate side-chains 196 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 171 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN B 340 ASN A 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.117582 restraints weight = 11518.670| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.84 r_work: 0.3455 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8640 Z= 0.168 Angle : 0.545 9.696 11723 Z= 0.286 Chirality : 0.043 0.170 1323 Planarity : 0.004 0.041 1492 Dihedral : 4.407 30.446 1174 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.94 % Allowed : 18.52 % Favored : 78.54 % 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: 0.88 (0.26), residues: 1061 helix: 2.22 (0.26), residues: 421 sheet: -0.41 (0.34), residues: 221 loop : -0.51 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.018 0.001 TYR R 100 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8635) covalent geometry : angle 0.54394 (11713) SS BOND : bond 0.00370 ( 5) SS BOND : angle 1.21551 ( 10) hydrogen bonds : bond 0.04163 ( 423) hydrogen bonds : angle 4.72529 ( 1200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: R 61 LYS cc_start: 0.7864 (mtpp) cc_final: 0.7658 (mtpp) REVERT: R 86 MET cc_start: 0.8128 (mtt) cc_final: 0.7780 (mtt) REVERT: R 94 VAL cc_start: 0.8328 (t) cc_final: 0.8067 (p) REVERT: R 292 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7786 (m-30) REVERT: B 101 MET cc_start: 0.8311 (mtt) cc_final: 0.7989 (mtm) REVERT: B 186 ASP cc_start: 0.7758 (m-30) cc_final: 0.7400 (m-30) REVERT: B 212 ASP cc_start: 0.7715 (t0) cc_final: 0.7296 (t0) REVERT: B 279 SER cc_start: 0.7277 (t) cc_final: 0.6964 (m) REVERT: N 32 TYR cc_start: 0.8565 (m-80) cc_final: 0.8307 (m-80) REVERT: N 53 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: A 16 LYS cc_start: 0.7977 (mttt) cc_final: 0.7291 (mttt) REVERT: A 20 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: A 26 ASP cc_start: 0.7577 (m-30) cc_final: 0.7294 (m-30) REVERT: A 27 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8199 (ttpt) REVERT: A 95 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8077 (mptp) REVERT: A 166 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7424 (mm-30) REVERT: A 171 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8106 (m) REVERT: A 195 ASP cc_start: 0.7939 (m-30) cc_final: 0.7617 (m-30) REVERT: A 201 SER cc_start: 0.8455 (t) cc_final: 0.8238 (p) outliers start: 27 outliers final: 15 residues processed: 190 average time/residue: 0.5554 time to fit residues: 112.6674 Evaluate side-chains 196 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 171 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 60 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.0070 chunk 100 optimal weight: 0.3980 chunk 40 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 20 ASN R 62 GLN B 340 ASN A 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.133849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.119247 restraints weight = 11484.706| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.84 r_work: 0.3480 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8640 Z= 0.119 Angle : 0.510 7.921 11723 Z= 0.268 Chirality : 0.042 0.155 1323 Planarity : 0.004 0.043 1492 Dihedral : 4.201 23.876 1174 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.16 % Allowed : 18.85 % Favored : 78.00 % 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: 1.06 (0.27), residues: 1061 helix: 2.38 (0.26), residues: 421 sheet: -0.28 (0.34), residues: 214 loop : -0.45 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 232 TYR 0.013 0.001 TYR R 309 PHE 0.012 0.001 PHE B 199 TRP 0.014 0.001 TRP A 96 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8635) covalent geometry : angle 0.50974 (11713) SS BOND : bond 0.00278 ( 5) SS BOND : angle 0.97879 ( 10) hydrogen bonds : bond 0.03681 ( 423) hydrogen bonds : angle 4.58190 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: R 20 ASN cc_start: 0.7938 (p0) cc_final: 0.7674 (p0) REVERT: R 86 MET cc_start: 0.8106 (mtt) cc_final: 0.7778 (mtt) REVERT: R 94 VAL cc_start: 0.8351 (t) cc_final: 0.8090 (p) REVERT: R 292 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: B 212 ASP cc_start: 0.7688 (t0) cc_final: 0.7266 (t0) REVERT: B 279 SER cc_start: 0.7125 (t) cc_final: 0.6831 (m) REVERT: B 318 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7996 (tt) REVERT: N 32 TYR cc_start: 0.8537 (m-80) cc_final: 0.8292 (m-80) REVERT: A 20 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: A 26 ASP cc_start: 0.7561 (m-30) cc_final: 0.7284 (m-30) REVERT: A 27 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8180 (ttpt) REVERT: A 91 ASP cc_start: 0.7982 (p0) cc_final: 0.7755 (p0) REVERT: A 166 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7343 (mm-30) REVERT: A 171 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8065 (m) REVERT: A 195 ASP cc_start: 0.7873 (m-30) cc_final: 0.7585 (m-30) REVERT: A 201 SER cc_start: 0.8427 (t) cc_final: 0.8201 (p) outliers start: 29 outliers final: 17 residues processed: 192 average time/residue: 0.5290 time to fit residues: 108.7862 Evaluate side-chains 192 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 171 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 0.0060 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN B 35 ASN B 340 ASN A 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.133935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119398 restraints weight = 11417.061| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.83 r_work: 0.3484 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8640 Z= 0.124 Angle : 0.526 12.373 11723 Z= 0.273 Chirality : 0.042 0.175 1323 Planarity : 0.004 0.044 1492 Dihedral : 4.167 24.521 1174 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.40 % Allowed : 19.28 % Favored : 78.32 % 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: 1.09 (0.27), residues: 1061 helix: 2.42 (0.26), residues: 421 sheet: -0.27 (0.34), residues: 214 loop : -0.43 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.012 0.001 TYR R 309 PHE 0.013 0.001 PHE B 199 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8635) covalent geometry : angle 0.52523 (11713) SS BOND : bond 0.00277 ( 5) SS BOND : angle 0.94007 ( 10) hydrogen bonds : bond 0.03672 ( 423) hydrogen bonds : angle 4.51800 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: R 86 MET cc_start: 0.8028 (mtt) cc_final: 0.7648 (mtt) REVERT: R 94 VAL cc_start: 0.8390 (t) cc_final: 0.8131 (p) REVERT: B 212 ASP cc_start: 0.7704 (t0) cc_final: 0.7277 (t0) REVERT: B 279 SER cc_start: 0.7137 (t) cc_final: 0.6837 (m) REVERT: B 318 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8096 (tt) REVERT: A 20 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: A 26 ASP cc_start: 0.7566 (m-30) cc_final: 0.7293 (m-30) REVERT: A 27 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8182 (ttpt) REVERT: A 166 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7348 (mm-30) REVERT: A 171 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8069 (m) REVERT: A 195 ASP cc_start: 0.7794 (m-30) cc_final: 0.7525 (m-30) REVERT: A 201 SER cc_start: 0.8431 (t) cc_final: 0.8209 (p) outliers start: 22 outliers final: 13 residues processed: 184 average time/residue: 0.5503 time to fit residues: 108.0093 Evaluate side-chains 189 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 171 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN B 35 ASN B 340 ASN A 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.133595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.118987 restraints weight = 11412.234| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.83 r_work: 0.3478 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8640 Z= 0.147 Angle : 0.542 11.372 11723 Z= 0.283 Chirality : 0.043 0.173 1323 Planarity : 0.004 0.043 1492 Dihedral : 4.264 26.318 1174 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.83 % Allowed : 18.63 % Favored : 78.54 % 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: 1.03 (0.27), residues: 1061 helix: 2.36 (0.26), residues: 421 sheet: -0.30 (0.34), residues: 214 loop : -0.46 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.016 0.001 TYR N 32 PHE 0.012 0.001 PHE B 199 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8635) covalent geometry : angle 0.54196 (11713) SS BOND : bond 0.00321 ( 5) SS BOND : angle 0.92353 ( 10) hydrogen bonds : bond 0.03859 ( 423) hydrogen bonds : angle 4.59656 ( 1200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: R 86 MET cc_start: 0.8058 (mtt) cc_final: 0.7668 (mtt) REVERT: R 94 VAL cc_start: 0.8340 (t) cc_final: 0.8090 (p) REVERT: R 292 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: B 186 ASP cc_start: 0.7772 (m-30) cc_final: 0.7366 (m-30) REVERT: B 212 ASP cc_start: 0.7726 (t0) cc_final: 0.7294 (t0) REVERT: B 279 SER cc_start: 0.7183 (t) cc_final: 0.6880 (m) REVERT: B 318 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8010 (tt) REVERT: A 20 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: A 26 ASP cc_start: 0.7563 (m-30) cc_final: 0.7287 (m-30) REVERT: A 27 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8176 (ttpt) REVERT: A 166 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 195 ASP cc_start: 0.7881 (m-30) cc_final: 0.7616 (m-30) REVERT: A 201 SER cc_start: 0.8437 (t) cc_final: 0.8222 (p) outliers start: 26 outliers final: 16 residues processed: 192 average time/residue: 0.5478 time to fit residues: 112.2704 Evaluate side-chains 191 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 161 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN R 132 GLN B 239 ASN B 340 ASN A 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119017 restraints weight = 11408.101| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.83 r_work: 0.3473 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8640 Z= 0.140 Angle : 0.531 10.940 11723 Z= 0.277 Chirality : 0.042 0.162 1323 Planarity : 0.004 0.043 1492 Dihedral : 4.247 25.871 1174 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.61 % Allowed : 19.17 % Favored : 78.21 % 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: 1.14 (0.27), residues: 1061 helix: 2.48 (0.26), residues: 415 sheet: -0.28 (0.34), residues: 213 loop : -0.36 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.013 0.001 TYR N 32 PHE 0.013 0.001 PHE B 199 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8635) covalent geometry : angle 0.53007 (11713) SS BOND : bond 0.00316 ( 5) SS BOND : angle 0.93729 ( 10) hydrogen bonds : bond 0.03796 ( 423) hydrogen bonds : angle 4.57079 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3488.42 seconds wall clock time: 60 minutes 11.38 seconds (3611.38 seconds total)