Starting phenix.real_space_refine on Tue Feb 3 22:16:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kt6_62557/02_2026/9kt6_62557.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kt6_62557/02_2026/9kt6_62557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kt6_62557/02_2026/9kt6_62557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kt6_62557/02_2026/9kt6_62557.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kt6_62557/02_2026/9kt6_62557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kt6_62557/02_2026/9kt6_62557.map" } resolution = 3.01 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= -0.000 sd= 0.002 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 57 5.16 5 C 4654 2.51 5 N 1244 2.21 5 O 1325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7280 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1830 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} 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: "R" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2382 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 281} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'P9X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.71, per 1000 atoms: 0.23 Number of scatterers: 7280 At special positions: 0 Unit cell: (76.59, 102.12, 136.16, 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 57 16.00 O 1325 8.00 N 1244 7.00 C 4654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " 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: 0.61 Conformation dependent library (CDL) restraints added in 273.3 milliseconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1736 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 44.3% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.862A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.672A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.751A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.603A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.543A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.526A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.596A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 55 removed outlier: 3.953A pdb=" N LYS R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 29 " --> pdb=" O PHE R 25 " (cutoff:3.500A) Proline residue: R 31 - end of helix removed outlier: 3.699A pdb=" N PHE R 54 " --> pdb=" O TRP R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 79 removed outlier: 3.547A pdb=" N ASN R 68 " --> pdb=" O ILE R 64 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU R 69 " --> pdb=" O PHE R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 89 Processing helix chain 'R' and resid 97 through 131 removed outlier: 4.759A pdb=" N VAL R 103 " --> pdb=" O PRO R 99 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA R 108 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN R 110 " --> pdb=" O MET R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 161 through 163 No H-bonds generated for 'chain 'R' and resid 161 through 163' Processing helix chain 'R' and resid 187 through 218 removed outlier: 4.315A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 224 through 262 removed outlier: 4.103A pdb=" N THR R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE R 233 " --> pdb=" O ALA R 229 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N MET R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 268 through 280 removed outlier: 4.279A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 284 Processing helix chain 'R' and resid 285 through 295 removed outlier: 3.526A pdb=" N LEU R 289 " --> pdb=" O MET R 285 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.799A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.144A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.834A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.150A 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: 6.887A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.077A 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: 3.653A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.644A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.614A 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: 3.553A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.049A 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: 3.767A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1026 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: 0.86 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1183 1.31 - 1.44: 2046 1.44 - 1.56: 4126 1.56 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 7435 Sorted by residual: bond pdb=" C1 P9X R 401 " pdb=" C2 P9X R 401 " ideal model delta sigma weight residual 1.550 1.356 0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" C4 P9X R 401 " pdb=" O1 P9X R 401 " ideal model delta sigma weight residual 1.342 1.519 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" C3 P9X R 401 " pdb=" C4 P9X R 401 " ideal model delta sigma weight residual 1.357 1.466 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C1 P9X R 401 " pdb=" O1 P9X R 401 " ideal model delta sigma weight residual 1.455 1.544 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C2 P9X R 401 " pdb=" C3 P9X R 401 " ideal model delta sigma weight residual 1.436 1.359 0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 7430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 9983 2.49 - 4.98: 63 4.98 - 7.47: 10 7.47 - 9.97: 4 9.97 - 12.46: 1 Bond angle restraints: 10061 Sorted by residual: angle pdb=" N SER R 91 " pdb=" CA SER R 91 " pdb=" C SER R 91 " ideal model delta sigma weight residual 107.88 113.85 -5.97 1.41e+00 5.03e-01 1.79e+01 angle pdb=" C1 P9X R 401 " pdb=" C2 P9X R 401 " pdb=" C3 P9X R 401 " ideal model delta sigma weight residual 105.43 117.89 -12.46 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C LYS R 15 " pdb=" CA LYS R 15 " pdb=" CB LYS R 15 " ideal model delta sigma weight residual 115.89 110.85 5.04 1.32e+00 5.74e-01 1.46e+01 angle pdb=" N GLY R 96 " pdb=" CA GLY R 96 " pdb=" C GLY R 96 " ideal model delta sigma weight residual 110.20 115.22 -5.02 1.32e+00 5.74e-01 1.45e+01 angle pdb=" N ASP R 92 " pdb=" CA ASP R 92 " pdb=" CB ASP R 92 " ideal model delta sigma weight residual 114.17 109.99 4.18 1.14e+00 7.69e-01 1.34e+01 ... (remaining 10056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 3967 17.88 - 35.77: 386 35.77 - 53.65: 65 53.65 - 71.53: 10 71.53 - 89.42: 6 Dihedral angle restraints: 4434 sinusoidal: 1765 harmonic: 2669 Sorted by residual: dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual 180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA MET C 21 " pdb=" C MET C 21 " pdb=" N GLU C 22 " pdb=" CA GLU C 22 " ideal model delta harmonic sigma weight residual 180.00 159.54 20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA PRO R 99 " pdb=" C PRO R 99 " pdb=" N CYS R 100 " pdb=" CA CYS R 100 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 4431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 884 0.047 - 0.095: 213 0.095 - 0.142: 43 0.142 - 0.190: 0 0.190 - 0.237: 1 Chirality restraints: 1141 Sorted by residual: chirality pdb=" C1 P9X R 401 " pdb=" C2 P9X R 401 " pdb=" C6 P9X R 401 " pdb=" O1 P9X R 401 " both_signs ideal model delta sigma weight residual False 2.77 2.54 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA MET C 21 " pdb=" N MET C 21 " pdb=" C MET C 21 " pdb=" CB MET C 21 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE R 13 " pdb=" N ILE R 13 " pdb=" C ILE R 13 " pdb=" CB ILE R 13 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1138 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 80 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO R 81 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO R 81 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 81 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 224 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C ALA R 224 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA R 224 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS R 225 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C THR B 87 " -0.023 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.008 2.00e-02 2.50e+03 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 50 2.64 - 3.20: 6307 3.20 - 3.77: 10632 3.77 - 4.33: 14750 4.33 - 4.90: 25147 Nonbonded interactions: 56886 Sorted by model distance: nonbonded pdb=" O LEU R 66 " pdb=" OH TYR R 295 " model vdw 2.069 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR R 284 " pdb=" O3 P9X R 401 " model vdw 2.281 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.301 3.120 nonbonded pdb=" O GLY R 262 " pdb=" OH TYR R 269 " model vdw 2.302 3.040 ... (remaining 56881 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=0.16 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 0.194 7438 Z= 0.218 Angle : 0.567 12.457 10067 Z= 0.302 Chirality : 0.041 0.237 1141 Planarity : 0.003 0.036 1269 Dihedral : 14.273 89.416 2689 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.29), residues: 906 helix: 2.35 (0.29), residues: 366 sheet: 1.18 (0.41), residues: 169 loop : -1.71 (0.28), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.008 0.001 TYR R 295 PHE 0.012 0.001 PHE R 107 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 7435) covalent geometry : angle 0.56696 (10061) SS BOND : bond 0.00184 ( 3) SS BOND : angle 0.67792 ( 6) hydrogen bonds : bond 0.15396 ( 357) hydrogen bonds : angle 5.96519 ( 1026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.255 Fit side-chains REVERT: C 21 MET cc_start: 0.6537 (ptp) cc_final: 0.6322 (ppp) REVERT: R 285 MET cc_start: 0.7763 (ttp) cc_final: 0.7448 (ttp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1366 time to fit residues: 16.0699 Evaluate side-chains 83 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.175116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112338 restraints weight = 8177.041| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.25 r_work: 0.2980 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7438 Z= 0.126 Angle : 0.505 5.614 10067 Z= 0.274 Chirality : 0.042 0.134 1141 Planarity : 0.004 0.045 1269 Dihedral : 4.643 38.925 1008 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.76 % Allowed : 6.68 % Favored : 92.57 % 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 (0.29), residues: 906 helix: 2.48 (0.29), residues: 358 sheet: 1.20 (0.41), residues: 169 loop : -1.59 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 15 TYR 0.021 0.001 TYR R 86 PHE 0.013 0.001 PHE B 199 TRP 0.014 0.001 TRP B 339 HIS 0.002 0.001 HIS R 184 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7435) covalent geometry : angle 0.50446 (10061) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.68440 ( 6) hydrogen bonds : bond 0.04083 ( 357) hydrogen bonds : angle 4.45306 ( 1026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.217 Fit side-chains REVERT: C 21 MET cc_start: 0.6948 (ptp) cc_final: 0.6402 (ppp) REVERT: R 301 PHE cc_start: 0.2811 (t80) cc_final: 0.2393 (t80) outliers start: 6 outliers final: 6 residues processed: 100 average time/residue: 0.1082 time to fit residues: 13.8497 Evaluate side-chains 92 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 217 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 48 optimal weight: 0.0040 chunk 53 optimal weight: 4.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.172242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.108246 restraints weight = 8118.352| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.16 r_work: 0.2916 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7438 Z= 0.174 Angle : 0.545 6.328 10067 Z= 0.295 Chirality : 0.044 0.139 1141 Planarity : 0.004 0.053 1269 Dihedral : 4.908 40.579 1008 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.64 % Allowed : 8.69 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.84 (0.29), residues: 906 helix: 2.31 (0.29), residues: 368 sheet: 1.07 (0.39), residues: 176 loop : -1.68 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.022 0.002 TYR B 105 PHE 0.016 0.002 PHE B 199 TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7435) covalent geometry : angle 0.54477 (10061) SS BOND : bond 0.00162 ( 3) SS BOND : angle 0.70448 ( 6) hydrogen bonds : bond 0.04604 ( 357) hydrogen bonds : angle 4.42734 ( 1026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.278 Fit side-chains REVERT: B 228 ASP cc_start: 0.8742 (m-30) cc_final: 0.8463 (m-30) REVERT: B 234 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8456 (t80) REVERT: C 21 MET cc_start: 0.6842 (ptp) cc_final: 0.6358 (ppp) REVERT: R 228 ARG cc_start: 0.6253 (tmt170) cc_final: 0.5634 (tmt170) REVERT: R 301 PHE cc_start: 0.3374 (t80) cc_final: 0.2975 (t80) outliers start: 13 outliers final: 12 residues processed: 101 average time/residue: 0.1007 time to fit residues: 12.9960 Evaluate side-chains 99 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 217 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.173507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112742 restraints weight = 8216.337| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.23 r_work: 0.2957 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7438 Z= 0.124 Angle : 0.494 6.370 10067 Z= 0.268 Chirality : 0.042 0.134 1141 Planarity : 0.004 0.051 1269 Dihedral : 4.734 43.451 1008 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.51 % Allowed : 10.71 % Favored : 87.78 % 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: 0.92 (0.29), residues: 906 helix: 2.47 (0.29), residues: 362 sheet: 1.01 (0.39), residues: 175 loop : -1.62 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 15 TYR 0.017 0.001 TYR R 86 PHE 0.013 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7435) covalent geometry : angle 0.49398 (10061) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.63039 ( 6) hydrogen bonds : bond 0.03874 ( 357) hydrogen bonds : angle 4.19979 ( 1026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.275 Fit side-chains REVERT: A 309 ASP cc_start: 0.8589 (t70) cc_final: 0.8372 (t0) REVERT: B 228 ASP cc_start: 0.8685 (m-30) cc_final: 0.8383 (m-30) REVERT: B 234 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8484 (t80) REVERT: C 21 MET cc_start: 0.6898 (ptp) cc_final: 0.6374 (ppp) REVERT: R 228 ARG cc_start: 0.6216 (tmt170) cc_final: 0.5600 (tmt170) REVERT: R 301 PHE cc_start: 0.3373 (t80) cc_final: 0.3044 (t80) outliers start: 12 outliers final: 10 residues processed: 102 average time/residue: 0.1136 time to fit residues: 14.9264 Evaluate side-chains 100 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 217 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.0670 chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.172851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.111206 restraints weight = 8107.444| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.37 r_work: 0.2947 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7438 Z= 0.137 Angle : 0.506 6.609 10067 Z= 0.274 Chirality : 0.042 0.154 1141 Planarity : 0.004 0.051 1269 Dihedral : 4.754 44.545 1008 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.89 % Allowed : 11.96 % Favored : 86.15 % 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: 0.91 (0.29), residues: 906 helix: 2.54 (0.29), residues: 359 sheet: 0.87 (0.39), residues: 178 loop : -1.61 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.016 0.001 TYR R 86 PHE 0.014 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7435) covalent geometry : angle 0.50629 (10061) SS BOND : bond 0.00147 ( 3) SS BOND : angle 0.62631 ( 6) hydrogen bonds : bond 0.03965 ( 357) hydrogen bonds : angle 4.18821 ( 1026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.285 Fit side-chains REVERT: A 52 GLN cc_start: 0.7776 (pm20) cc_final: 0.7456 (pm20) REVERT: B 217 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8171 (ptt) REVERT: B 228 ASP cc_start: 0.8672 (m-30) cc_final: 0.8302 (m-30) REVERT: B 234 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8580 (t80) REVERT: R 228 ARG cc_start: 0.6257 (tmt170) cc_final: 0.5698 (tmt170) REVERT: R 301 PHE cc_start: 0.3371 (t80) cc_final: 0.3091 (t80) outliers start: 15 outliers final: 13 residues processed: 105 average time/residue: 0.1149 time to fit residues: 15.3361 Evaluate side-chains 104 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 217 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.172952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109067 restraints weight = 8207.456| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.30 r_work: 0.2914 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7438 Z= 0.150 Angle : 0.519 6.671 10067 Z= 0.280 Chirality : 0.043 0.138 1141 Planarity : 0.004 0.050 1269 Dihedral : 4.828 45.727 1008 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.89 % Allowed : 13.22 % Favored : 84.89 % 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: 0.86 (0.29), residues: 906 helix: 2.49 (0.29), residues: 359 sheet: 0.82 (0.39), residues: 178 loop : -1.62 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 15 TYR 0.016 0.001 TYR R 86 PHE 0.015 0.002 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7435) covalent geometry : angle 0.51845 (10061) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.65931 ( 6) hydrogen bonds : bond 0.04132 ( 357) hydrogen bonds : angle 4.21210 ( 1026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.294 Fit side-chains REVERT: A 52 GLN cc_start: 0.7845 (pm20) cc_final: 0.7485 (pm20) REVERT: B 234 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8549 (t80) REVERT: R 228 ARG cc_start: 0.6270 (tmt170) cc_final: 0.5829 (tmt170) REVERT: R 301 PHE cc_start: 0.3370 (t80) cc_final: 0.3156 (t80) outliers start: 15 outliers final: 13 residues processed: 106 average time/residue: 0.1194 time to fit residues: 16.0533 Evaluate side-chains 102 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 217 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 54 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.173304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109152 restraints weight = 8185.111| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.30 r_work: 0.2925 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7438 Z= 0.131 Angle : 0.501 6.364 10067 Z= 0.271 Chirality : 0.042 0.147 1141 Planarity : 0.004 0.049 1269 Dihedral : 4.758 48.845 1008 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.14 % Allowed : 13.85 % Favored : 84.01 % 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: 0.91 (0.29), residues: 906 helix: 2.53 (0.29), residues: 360 sheet: 0.80 (0.39), residues: 178 loop : -1.58 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 15 TYR 0.015 0.001 TYR R 86 PHE 0.014 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7435) covalent geometry : angle 0.50076 (10061) SS BOND : bond 0.00147 ( 3) SS BOND : angle 0.60694 ( 6) hydrogen bonds : bond 0.03899 ( 357) hydrogen bonds : angle 4.14888 ( 1026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.296 Fit side-chains REVERT: A 52 GLN cc_start: 0.7851 (pm20) cc_final: 0.7456 (pm20) REVERT: B 217 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8237 (ptt) REVERT: B 234 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8516 (t80) REVERT: R 228 ARG cc_start: 0.6277 (tmt170) cc_final: 0.5834 (tmt170) outliers start: 17 outliers final: 15 residues processed: 104 average time/residue: 0.1256 time to fit residues: 16.4685 Evaluate side-chains 105 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 217 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 0.0870 chunk 71 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.109638 restraints weight = 8224.607| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.28 r_work: 0.2937 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7438 Z= 0.120 Angle : 0.492 6.432 10067 Z= 0.266 Chirality : 0.042 0.149 1141 Planarity : 0.004 0.050 1269 Dihedral : 4.685 49.547 1008 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.14 % Allowed : 14.48 % Favored : 83.38 % 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: 0.94 (0.29), residues: 906 helix: 2.53 (0.29), residues: 364 sheet: 0.79 (0.38), residues: 180 loop : -1.57 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 15 TYR 0.015 0.001 TYR R 86 PHE 0.013 0.001 PHE A 189 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7435) covalent geometry : angle 0.49191 (10061) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.62320 ( 6) hydrogen bonds : bond 0.03724 ( 357) hydrogen bonds : angle 4.10851 ( 1026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.293 Fit side-chains REVERT: A 52 GLN cc_start: 0.7887 (pm20) cc_final: 0.7423 (pm20) REVERT: B 217 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8091 (ptt) REVERT: B 234 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8535 (t80) REVERT: C 21 MET cc_start: 0.6755 (mpp) cc_final: 0.6499 (ppp) REVERT: R 228 ARG cc_start: 0.6319 (tmt170) cc_final: 0.5874 (tmt170) outliers start: 17 outliers final: 14 residues processed: 103 average time/residue: 0.1282 time to fit residues: 16.7216 Evaluate side-chains 106 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 217 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.171275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107058 restraints weight = 8120.558| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.25 r_work: 0.2889 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7438 Z= 0.186 Angle : 0.553 7.736 10067 Z= 0.299 Chirality : 0.044 0.155 1141 Planarity : 0.004 0.050 1269 Dihedral : 4.956 48.373 1008 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.27 % Allowed : 14.11 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.28), residues: 906 helix: 2.37 (0.29), residues: 363 sheet: 0.75 (0.38), residues: 181 loop : -1.66 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 15 TYR 0.014 0.001 TYR R 86 PHE 0.017 0.002 PHE B 199 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 7435) covalent geometry : angle 0.55249 (10061) SS BOND : bond 0.00181 ( 3) SS BOND : angle 0.71490 ( 6) hydrogen bonds : bond 0.04583 ( 357) hydrogen bonds : angle 4.32323 ( 1026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.208 Fit side-chains REVERT: B 217 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8191 (ptt) REVERT: B 234 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8557 (t80) outliers start: 18 outliers final: 15 residues processed: 102 average time/residue: 0.1220 time to fit residues: 15.8617 Evaluate side-chains 104 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 217 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.172239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.107831 restraints weight = 8205.881| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.28 r_work: 0.2895 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7438 Z= 0.159 Angle : 0.531 7.286 10067 Z= 0.288 Chirality : 0.043 0.153 1141 Planarity : 0.004 0.050 1269 Dihedral : 4.903 50.490 1008 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.02 % Allowed : 14.36 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.28), residues: 906 helix: 2.45 (0.29), residues: 360 sheet: 0.73 (0.38), residues: 181 loop : -1.69 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 15 TYR 0.024 0.001 TYR R 86 PHE 0.016 0.002 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7435) covalent geometry : angle 0.53068 (10061) SS BOND : bond 0.00165 ( 3) SS BOND : angle 0.68651 ( 6) hydrogen bonds : bond 0.04267 ( 357) hydrogen bonds : angle 4.24947 ( 1026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.301 Fit side-chains REVERT: B 234 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8437 (t80) REVERT: R 228 ARG cc_start: 0.6306 (tmt170) cc_final: 0.5755 (tmt170) outliers start: 16 outliers final: 15 residues processed: 99 average time/residue: 0.1286 time to fit residues: 16.0317 Evaluate side-chains 102 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 217 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 36 optimal weight: 0.0670 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.174164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109945 restraints weight = 8171.672| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.29 r_work: 0.2950 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7438 Z= 0.113 Angle : 0.490 6.305 10067 Z= 0.265 Chirality : 0.041 0.151 1141 Planarity : 0.004 0.050 1269 Dihedral : 4.728 52.871 1008 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.02 % Allowed : 14.23 % Favored : 83.75 % 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: 0.94 (0.29), residues: 906 helix: 2.59 (0.29), residues: 361 sheet: 0.85 (0.38), residues: 178 loop : -1.63 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 15 TYR 0.023 0.001 TYR R 86 PHE 0.013 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.001 0.000 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7435) covalent geometry : angle 0.48977 (10061) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.57848 ( 6) hydrogen bonds : bond 0.03633 ( 357) hydrogen bonds : angle 4.09235 ( 1026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2572.01 seconds wall clock time: 44 minutes 39.94 seconds (2679.94 seconds total)