Starting phenix.real_space_refine on Wed Aug 5 11:45:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/27xk_81535/08_2026/27xk_81535_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/27xk_81535/08_2026/27xk_81535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/27xk_81535/08_2026/27xk_81535_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/27xk_81535/08_2026/27xk_81535_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/27xk_81535/08_2026/27xk_81535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/27xk_81535/08_2026/27xk_81535.map" } resolution = 2.64 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= 0.065 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 59 5.16 5 C 6007 2.51 5 N 1632 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9440 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1973 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 238 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3218 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 1.81, per 1000 atoms: 0.19 Number of scatterers: 9440 At special positions: 0 Unit cell: (86.14, 100.74, 170.09, 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 59 16.00 O 1742 8.00 N 1632 7.00 C 6007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.25 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 230.7 milliseconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2230 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 41.5% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.655A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 246 through 250 removed outlier: 3.932A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.873A pdb=" N ARG A 284 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 317 removed outlier: 3.568A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.581A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 35 Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.532A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.745A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 91 through 95 Processing helix chain 'R' and resid 122 through 127 removed outlier: 4.179A pdb=" N CYS R 126 " --> pdb=" O ASP R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 169 removed outlier: 3.533A pdb=" N LEU R 141 " --> pdb=" O PRO R 137 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU R 144 " --> pdb=" O GLN R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 205 Processing helix chain 'R' and resid 223 through 257 removed outlier: 4.143A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 275 Processing helix chain 'R' and resid 276 through 279 Processing helix chain 'R' and resid 280 through 292 Processing helix chain 'R' and resid 306 through 338 Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 367 Processing helix chain 'R' and resid 381 through 403 removed outlier: 4.216A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.483A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50 removed outlier: 6.507A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.725A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.338A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.961A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.631A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.703A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.622A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.715A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 79 through 84 483 hydrogen bonds defined for protein. 1374 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: 1.54 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3071 1.34 - 1.46: 2297 1.46 - 1.58: 4206 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 9654 Sorted by residual: bond pdb=" N LYS C 34 " pdb=" CA LYS C 34 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.24e-02 6.50e+03 5.42e+00 bond pdb=" N GLY C 35 " pdb=" CA GLY C 35 " ideal model delta sigma weight residual 1.446 1.477 -0.031 1.54e-02 4.22e+03 3.98e+00 bond pdb=" N ARG C 36 " pdb=" CA ARG C 36 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.65e+00 bond pdb=" C VAL R 276 " pdb=" N PRO R 277 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.88e+00 bond pdb=" N LEU A 361 " pdb=" CA LEU A 361 " ideal model delta sigma weight residual 1.458 1.478 -0.020 1.90e-02 2.77e+03 1.08e+00 ... (remaining 9649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 12761 1.27 - 2.53: 261 2.53 - 3.80: 50 3.80 - 5.06: 11 5.06 - 6.33: 4 Bond angle restraints: 13087 Sorted by residual: angle pdb=" C GLU R 294 " pdb=" CA GLU R 294 " pdb=" CB GLU R 294 " ideal model delta sigma weight residual 115.79 110.01 5.78 1.19e+00 7.06e-01 2.36e+01 angle pdb=" C PHE R 367 " pdb=" N ALA R 368 " pdb=" CA ALA R 368 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" N THR R 343 " pdb=" CA THR R 343 " pdb=" C THR R 343 " ideal model delta sigma weight residual 113.43 109.95 3.48 1.26e+00 6.30e-01 7.63e+00 angle pdb=" CA LYS C 34 " pdb=" C LYS C 34 " pdb=" O LYS C 34 " ideal model delta sigma weight residual 120.55 118.06 2.49 1.07e+00 8.73e-01 5.43e+00 angle pdb=" O LEU B 51 " pdb=" C LEU B 51 " pdb=" N ARG B 52 " ideal model delta sigma weight residual 122.59 125.65 -3.06 1.33e+00 5.65e-01 5.29e+00 ... (remaining 13082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 5429 17.49 - 34.98: 223 34.98 - 52.47: 49 52.47 - 69.96: 9 69.96 - 87.45: 3 Dihedral angle restraints: 5713 sinusoidal: 2262 harmonic: 3451 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -56.99 -29.01 1 1.00e+01 1.00e-02 1.20e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual 93.00 66.08 26.92 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" N ARG R 102 " pdb=" CA ARG R 102 " pdb=" CB ARG R 102 " pdb=" CG ARG R 102 " ideal model delta sinusoidal sigma weight residual -60.00 -119.97 59.97 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1110 0.042 - 0.084: 268 0.084 - 0.126: 58 0.126 - 0.168: 7 0.168 - 0.210: 1 Chirality restraints: 1444 Sorted by residual: chirality pdb=" CA LEU A 361 " pdb=" N LEU A 361 " pdb=" C LEU A 361 " pdb=" CB LEU A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE A 255 " pdb=" N ILE A 255 " pdb=" C ILE A 255 " pdb=" CB ILE A 255 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ARG B 52 " pdb=" N ARG B 52 " pdb=" C ARG B 52 " pdb=" CB ARG B 52 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 1441 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 51 " 0.010 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C LEU B 51 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU B 51 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG B 52 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO G 53 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO R 277 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " -0.020 5.00e-02 4.00e+02 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 565 2.74 - 3.28: 9543 3.28 - 3.82: 16008 3.82 - 4.36: 18364 4.36 - 4.90: 32341 Nonbonded interactions: 76821 Sorted by model distance: nonbonded pdb=" OG SER R 155 " pdb=" O SER R 392 " model vdw 2.197 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.227 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.239 3.040 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.285 3.040 nonbonded pdb=" O TRP R 91 " pdb=" OG SER R 94 " model vdw 2.292 3.040 ... (remaining 76816 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: 3.170 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.050 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 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 : 0.003 0.219 9658 Z= 0.188 Angle : 0.563 31.156 13093 Z= 0.309 Chirality : 0.038 0.210 1444 Planarity : 0.003 0.040 1665 Dihedral : 10.285 87.452 3474 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.29 % Allowed : 7.46 % Favored : 92.25 % 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: 1.70 (0.26), residues: 1166 helix: 3.27 (0.25), residues: 433 sheet: 0.50 (0.34), residues: 225 loop : -0.51 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.010 0.001 TYR R 148 PHE 0.008 0.001 PHE A 189 TRP 0.008 0.001 TRP R 39 HIS 0.003 0.000 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.11 ( 9654) covalent geometry : angle 0.47557 / 0.27 (13087) SS BOND : bond 0.12625 / 6.31 ( 3) SS BOND : angle 14.07525 / 8.37 ( 6) hydrogen bonds : bond 0.12790 / 8.24 ( 483) hydrogen bonds : angle 4.59491 / 3.23 ( 1374) Misc. bond : bond 0.10639 / 5.60 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7267 (mmtm) cc_final: 0.6672 (mtmt) REVERT: A 24 GLN cc_start: 0.7240 (mm110) cc_final: 0.6995 (mm-40) REVERT: A 261 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7880 (mm110) REVERT: B 40 VAL cc_start: 0.5692 (p) cc_final: 0.5297 (t) REVERT: B 153 ASP cc_start: 0.7100 (p0) cc_final: 0.6889 (p0) REVERT: G 38 MET cc_start: 0.5044 (tpt) cc_final: 0.4573 (mtt) REVERT: N 59 SER cc_start: 0.5791 (m) cc_final: 0.5430 (t) REVERT: R 346 LYS cc_start: 0.7471 (mttm) cc_final: 0.7112 (mmpt) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.4784 time to fit residues: 99.1940 Evaluate side-chains 105 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.0070 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0060 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 24 GLN A 34 HIS ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 110 ASN B 220 GLN C 23 GLN N 120 GLN R 140 GLN R 173 HIS R 221 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 363 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.242676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.203913 restraints weight = 11138.414| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.01 r_work: 0.4102 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4001 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9658 Z= 0.107 Angle : 0.476 5.389 13093 Z= 0.255 Chirality : 0.040 0.177 1444 Planarity : 0.004 0.049 1665 Dihedral : 3.580 26.907 1297 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.75 % Allowed : 13.05 % Favored : 84.20 % 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: 1.76 (0.26), residues: 1166 helix: 3.30 (0.24), residues: 439 sheet: 0.60 (0.34), residues: 226 loop : -0.55 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 250 TYR 0.017 0.001 TYR R 148 PHE 0.013 0.001 PHE A 189 TRP 0.014 0.001 TRP R 420 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 ( 9654) covalent geometry : angle 0.47477 / 0.26 (13087) SS BOND : bond 0.00138 / 0.07 ( 3) SS BOND : angle 1.47158 / 0.87 ( 6) hydrogen bonds : bond 0.03587 / 2.35 ( 483) hydrogen bonds : angle 4.03841 / 2.87 ( 1374) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7278 (mmtm) cc_final: 0.6506 (mtpt) REVERT: A 24 GLN cc_start: 0.7427 (mm-40) cc_final: 0.6989 (mm-40) REVERT: A 325 TYR cc_start: 0.6586 (m-80) cc_final: 0.6177 (m-80) REVERT: B 59 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7253 (t80) REVERT: B 222 PHE cc_start: 0.4936 (OUTLIER) cc_final: 0.4020 (m-80) REVERT: B 311 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.6134 (t-170) REVERT: G 38 MET cc_start: 0.4950 (tpt) cc_final: 0.4215 (mtt) REVERT: N 80 TYR cc_start: 0.6013 (m-80) cc_final: 0.5808 (m-80) REVERT: R 145 TYR cc_start: 0.7119 (t80) cc_final: 0.6457 (t80) REVERT: R 346 LYS cc_start: 0.7629 (mttm) cc_final: 0.7222 (mmpt) REVERT: R 367 PHE cc_start: 0.5766 (OUTLIER) cc_final: 0.5220 (p90) REVERT: R 397 MET cc_start: 0.7742 (mtp) cc_final: 0.7394 (mtt) outliers start: 28 outliers final: 7 residues processed: 142 average time/residue: 0.4718 time to fit residues: 72.6559 Evaluate side-chains 111 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 352 SER Chi-restraints excluded: chain R residue 367 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 98 optimal weight: 0.0040 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 363 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.234231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.194160 restraints weight = 11144.610| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.06 r_work: 0.4019 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3914 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9658 Z= 0.117 Angle : 0.489 5.496 13093 Z= 0.262 Chirality : 0.040 0.160 1444 Planarity : 0.004 0.039 1665 Dihedral : 3.758 20.565 1297 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.85 % Allowed : 13.94 % 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: 1.67 (0.26), residues: 1166 helix: 3.17 (0.24), residues: 439 sheet: 0.50 (0.34), residues: 227 loop : -0.51 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 48 TYR 0.015 0.001 TYR R 148 PHE 0.018 0.002 PHE B 292 TRP 0.013 0.001 TRP A 248 HIS 0.007 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9654) covalent geometry : angle 0.48782 / 0.26 (13087) SS BOND : bond 0.00309 / 0.15 ( 3) SS BOND : angle 1.40632 / 0.65 ( 6) hydrogen bonds : bond 0.03549 / 2.31 ( 483) hydrogen bonds : angle 4.06702 / 2.89 ( 1374) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7316 (mmtm) cc_final: 0.6579 (mtpt) REVERT: A 24 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7071 (mm-40) REVERT: A 325 TYR cc_start: 0.6532 (m-80) cc_final: 0.6038 (m-80) REVERT: B 59 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7249 (t80) REVERT: B 134 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6693 (ptt180) REVERT: B 222 PHE cc_start: 0.5283 (OUTLIER) cc_final: 0.4277 (m-80) REVERT: B 270 ILE cc_start: 0.6544 (OUTLIER) cc_final: 0.6229 (pp) REVERT: B 311 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.6258 (t-170) REVERT: G 38 MET cc_start: 0.4934 (tpt) cc_final: 0.4142 (mtt) REVERT: R 325 VAL cc_start: 0.8377 (m) cc_final: 0.8121 (t) REVERT: R 346 LYS cc_start: 0.7771 (mttm) cc_final: 0.7209 (mmpt) REVERT: R 367 PHE cc_start: 0.5776 (OUTLIER) cc_final: 0.5158 (p90) outliers start: 29 outliers final: 12 residues processed: 136 average time/residue: 0.5122 time to fit residues: 75.2166 Evaluate side-chains 122 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 352 SER Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain R residue 373 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 0.0770 chunk 109 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 overall best weight: 1.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 ASN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.227949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.186400 restraints weight = 11110.843| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.41 r_work: 0.3912 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9658 Z= 0.163 Angle : 0.557 6.065 13093 Z= 0.298 Chirality : 0.042 0.150 1444 Planarity : 0.004 0.042 1665 Dihedral : 4.215 21.487 1297 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.51 % Allowed : 13.35 % Favored : 82.14 % 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: 1.36 (0.26), residues: 1166 helix: 2.83 (0.24), residues: 438 sheet: 0.15 (0.33), residues: 241 loop : -0.50 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 284 TYR 0.021 0.002 TYR R 148 PHE 0.018 0.002 PHE B 292 TRP 0.014 0.002 TRP R 243 HIS 0.008 0.002 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 9654) covalent geometry : angle 0.55645 / 0.30 (13087) SS BOND : bond 0.00260 / 0.13 ( 3) SS BOND : angle 1.06794 / 0.44 ( 6) hydrogen bonds : bond 0.04042 / 2.62 ( 483) hydrogen bonds : angle 4.42042 / 3.17 ( 1374) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7262 (mmtm) cc_final: 0.6513 (mtmt) REVERT: A 23 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7665 (mt) REVERT: A 24 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7149 (mm-40) REVERT: A 209 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8205 (ptt180) REVERT: B 59 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7371 (t80) REVERT: B 222 PHE cc_start: 0.5459 (OUTLIER) cc_final: 0.4547 (m-80) REVERT: B 270 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.6148 (pp) REVERT: B 311 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6467 (t-170) REVERT: B 325 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5831 (tpt) REVERT: G 38 MET cc_start: 0.4861 (tpt) cc_final: 0.4077 (mtt) REVERT: R 202 LYS cc_start: 0.6821 (ttmm) cc_final: 0.6412 (ttmm) REVERT: R 304 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.7157 (t0) REVERT: R 325 VAL cc_start: 0.8400 (m) cc_final: 0.8129 (t) REVERT: R 346 LYS cc_start: 0.7881 (mttm) cc_final: 0.7268 (mmtt) REVERT: R 351 LYS cc_start: 0.7676 (ttpp) cc_final: 0.7245 (ttmm) REVERT: R 367 PHE cc_start: 0.5892 (OUTLIER) cc_final: 0.5204 (p90) outliers start: 46 outliers final: 11 residues processed: 148 average time/residue: 0.4696 time to fit residues: 75.3886 Evaluate side-chains 124 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 352 SER Chi-restraints excluded: chain R residue 367 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 113 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.228444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.186772 restraints weight = 11091.529| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.12 r_work: 0.3936 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9658 Z= 0.127 Angle : 0.512 7.270 13093 Z= 0.276 Chirality : 0.041 0.147 1444 Planarity : 0.004 0.038 1665 Dihedral : 4.245 30.902 1297 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.02 % Allowed : 15.31 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.39 (0.25), residues: 1166 helix: 2.96 (0.24), residues: 432 sheet: 0.11 (0.32), residues: 249 loop : -0.53 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 250 TYR 0.022 0.001 TYR R 148 PHE 0.015 0.002 PHE A 189 TRP 0.014 0.001 TRP R 243 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9654) covalent geometry : angle 0.50758 / 0.27 (13087) SS BOND : bond 0.00831 / 0.40 ( 3) SS BOND : angle 3.04377 / 1.29 ( 6) hydrogen bonds : bond 0.03677 / 2.38 ( 483) hydrogen bonds : angle 4.26636 / 3.05 ( 1374) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 102 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7312 (mmtm) cc_final: 0.6594 (mtmt) REVERT: A 24 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7153 (mm-40) REVERT: A 229 ASP cc_start: 0.7056 (t70) cc_final: 0.6598 (t70) REVERT: A 239 ASP cc_start: 0.6831 (m-30) cc_final: 0.6596 (m-30) REVERT: A 294 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6416 (mt-10) REVERT: B 59 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7273 (t80) REVERT: B 222 PHE cc_start: 0.5373 (OUTLIER) cc_final: 0.4517 (m-80) REVERT: B 270 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6048 (pp) REVERT: B 311 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.6302 (t-170) REVERT: B 318 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7294 (mp) REVERT: G 38 MET cc_start: 0.4950 (tpt) cc_final: 0.4150 (mtt) REVERT: R 148 TYR cc_start: 0.7952 (p90) cc_final: 0.7697 (p90) REVERT: R 202 LYS cc_start: 0.6857 (ttmm) cc_final: 0.6464 (ttmm) REVERT: R 304 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.7121 (t0) REVERT: R 325 VAL cc_start: 0.8377 (m) cc_final: 0.8140 (t) REVERT: R 346 LYS cc_start: 0.7905 (mttm) cc_final: 0.7287 (mmtt) REVERT: R 351 LYS cc_start: 0.7746 (ttpp) cc_final: 0.7244 (ttmm) REVERT: R 367 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.5184 (p90) outliers start: 41 outliers final: 16 residues processed: 132 average time/residue: 0.4431 time to fit residues: 63.3355 Evaluate side-chains 124 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 352 SER Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain R residue 373 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 74 optimal weight: 0.3980 chunk 113 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN A 246 ASN ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.226150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.184150 restraints weight = 11021.755| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.25 r_work: 0.3890 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9658 Z= 0.157 Angle : 0.551 8.190 13093 Z= 0.296 Chirality : 0.042 0.137 1444 Planarity : 0.004 0.038 1665 Dihedral : 4.360 23.806 1297 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.32 % Allowed : 15.60 % Favored : 80.08 % 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: 1.25 (0.25), residues: 1166 helix: 2.83 (0.24), residues: 431 sheet: 0.03 (0.33), residues: 241 loop : -0.58 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 250 TYR 0.020 0.002 TYR R 148 PHE 0.015 0.002 PHE B 151 TRP 0.016 0.002 TRP R 243 HIS 0.007 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 9654) covalent geometry : angle 0.54785 / 0.29 (13087) SS BOND : bond 0.01196 / 0.57 ( 3) SS BOND : angle 2.78255 / 1.20 ( 6) hydrogen bonds : bond 0.03972 / 2.56 ( 483) hydrogen bonds : angle 4.44437 / 3.19 ( 1374) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7265 (mmtm) cc_final: 0.6523 (mtmt) REVERT: A 23 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7624 (mt) REVERT: A 24 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7182 (mm-40) REVERT: A 178 ARG cc_start: 0.5583 (OUTLIER) cc_final: 0.5127 (mmt90) REVERT: A 229 ASP cc_start: 0.7119 (t70) cc_final: 0.6626 (t70) REVERT: A 239 ASP cc_start: 0.6786 (m-30) cc_final: 0.6541 (m-30) REVERT: A 294 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6426 (mt-10) REVERT: B 59 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7284 (t80) REVERT: B 222 PHE cc_start: 0.5504 (OUTLIER) cc_final: 0.4661 (m-80) REVERT: B 311 HIS cc_start: 0.6900 (OUTLIER) cc_final: 0.6440 (t-170) REVERT: B 340 ASN cc_start: 0.7245 (t0) cc_final: 0.6938 (m-40) REVERT: G 38 MET cc_start: 0.4940 (tpt) cc_final: 0.4140 (mtt) REVERT: N 19 ARG cc_start: 0.6544 (tpt170) cc_final: 0.6126 (tpt170) REVERT: R 148 TYR cc_start: 0.8024 (p90) cc_final: 0.7750 (p90) REVERT: R 202 LYS cc_start: 0.6777 (ttmm) cc_final: 0.6386 (ttmm) REVERT: R 304 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.7165 (t0) REVERT: R 325 VAL cc_start: 0.8380 (m) cc_final: 0.8102 (t) REVERT: R 346 LYS cc_start: 0.7969 (mttm) cc_final: 0.7295 (mmtt) REVERT: R 351 LYS cc_start: 0.7774 (ttpp) cc_final: 0.7267 (ttmm) REVERT: R 367 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.5155 (p90) REVERT: R 384 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6734 (mp) outliers start: 44 outliers final: 19 residues processed: 142 average time/residue: 0.4227 time to fit residues: 65.0540 Evaluate side-chains 129 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 352 SER Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.0270 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN B 220 GLN ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.228515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.187558 restraints weight = 11143.117| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.07 r_work: 0.3931 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9658 Z= 0.110 Angle : 0.499 7.672 13093 Z= 0.270 Chirality : 0.040 0.156 1444 Planarity : 0.004 0.040 1665 Dihedral : 4.171 23.317 1297 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.53 % Allowed : 16.39 % Favored : 80.08 % 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: 1.40 (0.25), residues: 1166 helix: 3.02 (0.24), residues: 432 sheet: 0.24 (0.33), residues: 231 loop : -0.63 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 48 TYR 0.022 0.001 TYR A 325 PHE 0.014 0.001 PHE A 189 TRP 0.017 0.001 TRP R 420 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9654) covalent geometry : angle 0.49736 / 0.27 (13087) SS BOND : bond 0.00568 / 0.27 ( 3) SS BOND : angle 2.16813 / 0.93 ( 6) hydrogen bonds : bond 0.03499 / 2.27 ( 483) hydrogen bonds : angle 4.21590 / 3.02 ( 1374) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7330 (mmtm) cc_final: 0.6609 (mtmt) REVERT: A 23 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7623 (mt) REVERT: A 24 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7210 (mm-40) REVERT: A 229 ASP cc_start: 0.7073 (t70) cc_final: 0.6588 (t70) REVERT: A 239 ASP cc_start: 0.6780 (m-30) cc_final: 0.6546 (m-30) REVERT: A 294 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6335 (mt-10) REVERT: B 59 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7267 (t80) REVERT: B 222 PHE cc_start: 0.5410 (OUTLIER) cc_final: 0.4581 (m-80) REVERT: B 311 HIS cc_start: 0.6716 (OUTLIER) cc_final: 0.6142 (t-170) REVERT: B 318 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7319 (mp) REVERT: B 325 MET cc_start: 0.6284 (mtt) cc_final: 0.6080 (OUTLIER) REVERT: G 38 MET cc_start: 0.4964 (tpt) cc_final: 0.4175 (mtt) REVERT: N 19 ARG cc_start: 0.6536 (tpt170) cc_final: 0.6202 (tpt170) REVERT: R 148 TYR cc_start: 0.7961 (p90) cc_final: 0.7707 (p90) REVERT: R 202 LYS cc_start: 0.6761 (ttmm) cc_final: 0.6377 (ttmm) REVERT: R 304 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.7162 (t0) REVERT: R 346 LYS cc_start: 0.8011 (mttm) cc_final: 0.7325 (mmtt) REVERT: R 351 LYS cc_start: 0.7738 (ttpp) cc_final: 0.7232 (ttmm) REVERT: R 367 PHE cc_start: 0.5885 (OUTLIER) cc_final: 0.5157 (p90) REVERT: R 384 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6714 (mp) outliers start: 36 outliers final: 18 residues processed: 136 average time/residue: 0.5009 time to fit residues: 73.7914 Evaluate side-chains 123 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 0.0070 chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.6804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN B 220 GLN ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.227507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.185905 restraints weight = 11083.037| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 2.09 r_work: 0.3920 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9658 Z= 0.122 Angle : 0.509 8.236 13093 Z= 0.274 Chirality : 0.040 0.175 1444 Planarity : 0.004 0.039 1665 Dihedral : 4.147 21.628 1297 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.53 % Allowed : 16.68 % Favored : 79.78 % 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: 1.43 (0.25), residues: 1166 helix: 3.06 (0.24), residues: 432 sheet: 0.37 (0.33), residues: 226 loop : -0.68 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 209 TYR 0.020 0.001 TYR R 148 PHE 0.013 0.002 PHE A 189 TRP 0.017 0.001 TRP R 420 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 9654) covalent geometry : angle 0.50723 / 0.27 (13087) SS BOND : bond 0.00635 / 0.31 ( 3) SS BOND : angle 2.13598 / 0.93 ( 6) hydrogen bonds : bond 0.03601 / 2.33 ( 483) hydrogen bonds : angle 4.21192 / 3.02 ( 1374) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7334 (mmtm) cc_final: 0.6607 (mtmt) REVERT: A 23 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7635 (mt) REVERT: A 24 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7188 (mm-40) REVERT: A 178 ARG cc_start: 0.5559 (OUTLIER) cc_final: 0.5108 (mmt90) REVERT: A 229 ASP cc_start: 0.7081 (t70) cc_final: 0.6609 (t70) REVERT: A 239 ASP cc_start: 0.6714 (m-30) cc_final: 0.6457 (m-30) REVERT: A 294 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6370 (mt-10) REVERT: B 59 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7270 (t80) REVERT: B 222 PHE cc_start: 0.5421 (OUTLIER) cc_final: 0.4593 (m-80) REVERT: B 311 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.6240 (t-170) REVERT: B 318 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7391 (mp) REVERT: B 340 ASN cc_start: 0.7128 (t0) cc_final: 0.6820 (m-40) REVERT: G 38 MET cc_start: 0.4904 (tpt) cc_final: 0.4106 (mtt) REVERT: R 83 VAL cc_start: 0.4639 (OUTLIER) cc_final: 0.4407 (t) REVERT: R 148 TYR cc_start: 0.7974 (p90) cc_final: 0.7724 (p90) REVERT: R 202 LYS cc_start: 0.6767 (ttmm) cc_final: 0.6368 (ttmm) REVERT: R 304 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7156 (t0) REVERT: R 346 LYS cc_start: 0.8020 (mttm) cc_final: 0.7370 (mmpt) REVERT: R 351 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7241 (ttmm) REVERT: R 367 PHE cc_start: 0.5870 (OUTLIER) cc_final: 0.5112 (p90) REVERT: R 384 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6673 (mp) outliers start: 36 outliers final: 18 residues processed: 131 average time/residue: 0.5067 time to fit residues: 71.8275 Evaluate side-chains 125 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 55 optimal weight: 0.7980 chunk 85 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN B 220 GLN ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.227365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.185938 restraints weight = 11036.395| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.10 r_work: 0.3932 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9658 Z= 0.127 Angle : 0.513 8.483 13093 Z= 0.275 Chirality : 0.041 0.173 1444 Planarity : 0.004 0.039 1665 Dihedral : 4.124 21.206 1297 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.34 % Allowed : 16.68 % Favored : 79.98 % 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: 1.42 (0.25), residues: 1166 helix: 3.04 (0.24), residues: 432 sheet: 0.30 (0.33), residues: 229 loop : -0.65 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 227 TYR 0.020 0.001 TYR A 325 PHE 0.015 0.002 PHE N 108 TRP 0.016 0.001 TRP R 420 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9654) covalent geometry : angle 0.51220 / 0.27 (13087) SS BOND : bond 0.00186 / 0.09 ( 3) SS BOND : angle 1.49492 / 0.66 ( 6) hydrogen bonds : bond 0.03638 / 2.36 ( 483) hydrogen bonds : angle 4.24100 / 3.04 ( 1374) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7294 (mmtm) cc_final: 0.6553 (mtmt) REVERT: A 23 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7646 (mt) REVERT: A 24 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7202 (mm-40) REVERT: A 178 ARG cc_start: 0.5665 (OUTLIER) cc_final: 0.5184 (mmt90) REVERT: A 229 ASP cc_start: 0.7030 (t70) cc_final: 0.6542 (t70) REVERT: A 289 GLU cc_start: 0.7201 (mp0) cc_final: 0.6984 (mp0) REVERT: A 294 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6343 (mt-10) REVERT: B 59 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7263 (t80) REVERT: B 222 PHE cc_start: 0.5461 (OUTLIER) cc_final: 0.4619 (m-80) REVERT: B 311 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.6213 (t-170) REVERT: B 318 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7408 (mp) REVERT: B 325 MET cc_start: 0.6225 (mtt) cc_final: 0.5939 (tpp) REVERT: B 340 ASN cc_start: 0.7151 (t0) cc_final: 0.6852 (m-40) REVERT: G 38 MET cc_start: 0.4892 (tpt) cc_final: 0.4099 (mtt) REVERT: N 19 ARG cc_start: 0.6490 (tpt170) cc_final: 0.6267 (tpt170) REVERT: R 83 VAL cc_start: 0.4620 (OUTLIER) cc_final: 0.4397 (t) REVERT: R 202 LYS cc_start: 0.6749 (ttmm) cc_final: 0.6355 (ttmm) REVERT: R 222 ASP cc_start: 0.7127 (t0) cc_final: 0.6368 (m-30) REVERT: R 304 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.7082 (t0) REVERT: R 346 LYS cc_start: 0.8026 (mttm) cc_final: 0.7363 (mmpt) REVERT: R 351 LYS cc_start: 0.7760 (ttpp) cc_final: 0.7256 (ttmm) REVERT: R 384 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6682 (mp) outliers start: 34 outliers final: 18 residues processed: 125 average time/residue: 0.5038 time to fit residues: 68.2496 Evaluate side-chains 123 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 21 optimal weight: 0.0030 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN B 220 GLN ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.224556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.182716 restraints weight = 11081.719| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.19 r_work: 0.3872 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9658 Z= 0.161 Angle : 0.560 9.372 13093 Z= 0.299 Chirality : 0.042 0.174 1444 Planarity : 0.004 0.038 1665 Dihedral : 4.358 22.100 1297 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.14 % Allowed : 16.98 % Favored : 79.88 % 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: 1.23 (0.25), residues: 1166 helix: 2.88 (0.24), residues: 432 sheet: -0.02 (0.33), residues: 240 loop : -0.63 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 227 TYR 0.025 0.002 TYR A 325 PHE 0.015 0.002 PHE B 151 TRP 0.020 0.002 TRP R 420 HIS 0.007 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 9654) covalent geometry : angle 0.55762 / 0.30 (13087) SS BOND : bond 0.00577 / 0.28 ( 3) SS BOND : angle 2.50701 / 1.08 ( 6) hydrogen bonds : bond 0.04038 / 2.61 ( 483) hydrogen bonds : angle 4.45390 / 3.21 ( 1374) Misc. bond : bond 0.00006 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6263 (pp20) REVERT: A 17 LYS cc_start: 0.7286 (mmtm) cc_final: 0.6561 (mtmt) REVERT: A 23 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7651 (mt) REVERT: A 24 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7209 (mm-40) REVERT: A 178 ARG cc_start: 0.5651 (OUTLIER) cc_final: 0.5190 (mmt90) REVERT: A 229 ASP cc_start: 0.7147 (t70) cc_final: 0.6655 (t70) REVERT: A 294 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6378 (mt-10) REVERT: B 59 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7301 (t80) REVERT: B 222 PHE cc_start: 0.5687 (OUTLIER) cc_final: 0.4838 (m-80) REVERT: B 311 HIS cc_start: 0.6925 (OUTLIER) cc_final: 0.6496 (t-170) REVERT: B 318 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7538 (mp) REVERT: B 325 MET cc_start: 0.6389 (mtt) cc_final: 0.5929 (tpt) REVERT: B 340 ASN cc_start: 0.7138 (t0) cc_final: 0.6820 (m-40) REVERT: G 38 MET cc_start: 0.4934 (tpt) cc_final: 0.4104 (mtt) REVERT: R 83 VAL cc_start: 0.4620 (OUTLIER) cc_final: 0.4395 (t) REVERT: R 202 LYS cc_start: 0.6711 (ttmm) cc_final: 0.6303 (ttmm) REVERT: R 222 ASP cc_start: 0.7183 (t0) cc_final: 0.6430 (m-30) REVERT: R 304 ASN cc_start: 0.7412 (OUTLIER) cc_final: 0.7104 (t0) REVERT: R 346 LYS cc_start: 0.8033 (mttm) cc_final: 0.7372 (mmpt) REVERT: R 351 LYS cc_start: 0.7800 (ttpp) cc_final: 0.7294 (ttmm) outliers start: 32 outliers final: 20 residues processed: 126 average time/residue: 0.4846 time to fit residues: 66.0005 Evaluate side-chains 127 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 304 ASN Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 352 SER Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN B 220 GLN ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.225741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.184323 restraints weight = 10947.880| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.05 r_work: 0.3909 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9658 Z= 0.142 Angle : 0.542 12.807 13093 Z= 0.288 Chirality : 0.041 0.168 1444 Planarity : 0.004 0.038 1665 Dihedral : 4.304 21.638 1297 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.24 % Allowed : 16.58 % Favored : 80.18 % 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: 1.26 (0.25), residues: 1166 helix: 2.90 (0.24), residues: 432 sheet: 0.17 (0.34), residues: 230 loop : -0.71 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 227 TYR 0.025 0.002 TYR R 148 PHE 0.022 0.002 PHE B 292 TRP 0.028 0.002 TRP R 420 HIS 0.007 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 9654) covalent geometry : angle 0.53923 / 0.29 (13087) SS BOND : bond 0.00466 / 0.23 ( 3) SS BOND : angle 2.69880 / 1.17 ( 6) hydrogen bonds : bond 0.03835 / 2.49 ( 483) hydrogen bonds : angle 4.39572 / 3.16 ( 1374) Misc. bond : bond 0.00007 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4136.64 seconds wall clock time: 71 minutes 4.98 seconds (4264.98 seconds total)