Starting phenix.real_space_refine on Fri Sep 11 02:44:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6d9h_7835/09_2026/6d9h_7835.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d9h_7835/09_2026/6d9h_7835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6d9h_7835/09_2026/6d9h_7835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d9h_7835/09_2026/6d9h_7835.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6d9h_7835/09_2026/6d9h_7835.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6d9h_7835/09_2026/6d9h_7835.cif" model { file = "/net/cci-nas-00/data/ceres_data/6d9h_7835/09_2026/6d9h_7835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d9h_7835/09_2026/6d9h_7835.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 52 5.16 5 C 4503 2.51 5 N 1196 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7023 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1691 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 206} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2276 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 14, 'TRANS': 273} Chain breaks: 1 Chain: "R" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 1.57, per 1000 atoms: 0.22 Number of scatterers: 7023 At special positions: 0 Unit cell: (76.32, 139.92, 100.7, 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 52 16.00 O 1272 8.00 N 1196 7.00 C 4503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 80 " - pdb=" SG CYS R 169 " distance=2.03 Simple disulfide: pdb=" SG CYS R 260 " - pdb=" SG CYS R 263 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 474.6 milliseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 49.2% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 removed outlier: 4.203A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.770A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.171A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 removed outlier: 3.610A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.170A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 4.094A pdb=" N THR A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.909A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 330 through 353 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.900A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.550A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 37 Proline residue: R 25 - end of helix removed outlier: 3.737A pdb=" N ASN R 37 " --> pdb=" O ALA R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 72 removed outlier: 4.860A pdb=" N ILE R 63 " --> pdb=" O GLY R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'R' and resid 77 through 111 Proline residue: R 86 - end of helix removed outlier: 3.623A pdb=" N SER R 93 " --> pdb=" O ILE R 89 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL R 109 " --> pdb=" O ARG R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 119 Processing helix chain 'R' and resid 120 through 141 Processing helix chain 'R' and resid 148 through 160 Processing helix chain 'R' and resid 170 through 175 Processing helix chain 'R' and resid 176 through 182 Processing helix chain 'R' and resid 182 through 189 removed outlier: 3.825A pdb=" N VAL R 189 " --> pdb=" O PHE R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 213 Processing helix chain 'R' and resid 224 through 260 removed outlier: 3.610A pdb=" N LEU R 248 " --> pdb=" O ALA R 244 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 266 through 289 removed outlier: 4.025A pdb=" N THR R 270 " --> pdb=" O PRO R 266 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER R 281 " --> pdb=" O THR R 277 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA R 282 " --> pdb=" O HIS R 278 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 292 through 301 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 6.976A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ALA A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.885A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.666A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.514A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.294A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.912A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.660A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.090A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 74 through 76 396 hydrogen bonds defined for protein. 1161 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: 1.09 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2229 1.34 - 1.46: 1578 1.46 - 1.58: 3283 1.58 - 1.70: 0 1.70 - 1.82: 75 Bond restraints: 7165 Sorted by residual: bond pdb=" C VAL R 24 " pdb=" N PRO R 25 " ideal model delta sigma weight residual 1.335 1.364 -0.028 1.36e-02 5.41e+03 4.32e+00 bond pdb=" C THR R 141 " pdb=" N PRO R 142 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.54e+00 bond pdb=" C CYS R 85 " pdb=" N PRO R 86 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.19e-02 7.06e+03 3.20e+00 bond pdb=" CA CYS R 85 " pdb=" C CYS R 85 " ideal model delta sigma weight residual 1.524 1.546 -0.022 1.26e-02 6.30e+03 3.15e+00 bond pdb=" CG LEU B 192 " pdb=" CD1 LEU B 192 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.09e+00 ... (remaining 7160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 9283 1.97 - 3.94: 349 3.94 - 5.91: 50 5.91 - 7.89: 19 7.89 - 9.86: 5 Bond angle restraints: 9706 Sorted by residual: angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 130.04 -8.50 1.91e+00 2.74e-01 1.98e+01 angle pdb=" CA LYS R 35 " pdb=" CB LYS R 35 " pdb=" CG LYS R 35 " ideal model delta sigma weight residual 114.10 122.70 -8.60 2.00e+00 2.50e-01 1.85e+01 angle pdb=" C ILE R 274 " pdb=" N PHE R 275 " pdb=" CA PHE R 275 " ideal model delta sigma weight residual 121.14 113.92 7.22 1.75e+00 3.27e-01 1.70e+01 angle pdb=" N LEU R 248 " pdb=" CA LEU R 248 " pdb=" C LEU R 248 " ideal model delta sigma weight residual 113.16 118.55 -5.39 1.42e+00 4.96e-01 1.44e+01 angle pdb=" C PHE G 61 " pdb=" N ARG G 62 " pdb=" CA ARG G 62 " ideal model delta sigma weight residual 121.70 128.51 -6.81 1.80e+00 3.09e-01 1.43e+01 ... (remaining 9701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 4077 15.22 - 30.44: 145 30.44 - 45.66: 43 45.66 - 60.88: 2 60.88 - 76.10: 4 Dihedral angle restraints: 4271 sinusoidal: 1669 harmonic: 2602 Sorted by residual: dihedral pdb=" CA GLY A 293 " pdb=" C GLY A 293 " pdb=" N ALA A 294 " pdb=" CA ALA A 294 " ideal model delta harmonic sigma weight residual 180.00 -154.06 -25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 4268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 837 0.058 - 0.116: 231 0.116 - 0.174: 45 0.174 - 0.232: 10 0.232 - 0.291: 2 Chirality restraints: 1125 Sorted by residual: chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA PHE R 275 " pdb=" N PHE R 275 " pdb=" C PHE R 275 " pdb=" CB PHE R 275 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA LYS R 35 " pdb=" N LYS R 35 " pdb=" C LYS R 35 " pdb=" CB LYS R 35 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1122 not shown) Planarity restraints: 1213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 181 " 0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C VAL R 181 " -0.087 2.00e-02 2.50e+03 pdb=" O VAL R 181 " 0.032 2.00e-02 2.50e+03 pdb=" N TYR R 182 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 182 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C TYR R 182 " 0.057 2.00e-02 2.50e+03 pdb=" O TYR R 182 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE R 183 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 146 " 0.025 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP R 146 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP R 146 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP R 146 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 146 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 146 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP R 146 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 146 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 146 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 146 " 0.018 2.00e-02 2.50e+03 ... (remaining 1210 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 774 2.76 - 3.29: 6666 3.29 - 3.83: 11421 3.83 - 4.36: 12948 4.36 - 4.90: 23105 Nonbonded interactions: 54914 Sorted by model distance: nonbonded pdb=" OD1 ASP R 55 " pdb=" OG SER R 281 " model vdw 2.219 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.263 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.282 3.040 nonbonded pdb=" O ILE B 123 " pdb=" OG SER B 136 " model vdw 2.298 3.040 nonbonded pdb=" OG1 THR R 44 " pdb=" OD2 ASP R 104 " model vdw 2.335 3.040 ... (remaining 54909 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 group one per residue 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: 0.520 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.760 Find NCS groups from input model: 0.040 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 7167 Z= 0.272 Angle : 0.932 9.857 9710 Z= 0.518 Chirality : 0.056 0.291 1125 Planarity : 0.007 0.050 1213 Dihedral : 9.324 76.099 2573 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -1.52 (0.25), residues: 876 helix: 0.08 (0.23), residues: 404 sheet: -0.57 (0.39), residues: 154 loop : -2.65 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.021 0.003 TYR R 179 PHE 0.039 0.004 PHE R 171 TRP 0.049 0.004 TRP R 146 HIS 0.007 0.002 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.27 ( 7165) covalent geometry : angle 0.93186 / 0.52 ( 9706) SS BOND : bond 0.00275 / 0.14 ( 2) SS BOND : angle 1.44368 / 0.91 ( 4) hydrogen bonds : bond 0.11970 / 8.14 ( 396) hydrogen bonds : angle 5.90794 / 4.10 ( 1161) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8049 (m-40) cc_final: 0.7667 (m110) REVERT: B 118 ASP cc_start: 0.7416 (p0) cc_final: 0.7063 (t0) REVERT: R 89 ILE cc_start: 0.8617 (mt) cc_final: 0.8366 (mt) REVERT: R 117 MET cc_start: 0.7175 (ptm) cc_final: 0.6953 (mmm) REVERT: R 275 PHE cc_start: 0.8534 (p90) cc_final: 0.7706 (p90) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.0879 time to fit residues: 22.3273 Evaluate side-chains 128 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 196 HIS A 295 ASN A 332 ASN B 6 GLN B 88 ASN B 239 ASN B 266 HIS R 38 GLN R 184 ASN R 251 HIS R 280 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129287 restraints weight = 7713.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130483 restraints weight = 7144.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131605 restraints weight = 6105.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.132132 restraints weight = 5357.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133740 restraints weight = 4868.666| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7167 Z= 0.192 Angle : 0.595 5.875 9710 Z= 0.324 Chirality : 0.044 0.179 1125 Planarity : 0.005 0.065 1213 Dihedral : 4.727 21.196 954 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.71 % Allowed : 9.20 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.28), residues: 876 helix: 1.12 (0.25), residues: 414 sheet: -0.45 (0.38), residues: 164 loop : -2.23 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 108 TYR 0.016 0.002 TYR G 40 PHE 0.037 0.002 PHE R 275 TRP 0.027 0.003 TRP R 146 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 ( 7165) covalent geometry : angle 0.59441 / 0.32 ( 9706) SS BOND : bond 0.00139 / 0.07 ( 2) SS BOND : angle 0.83766 / 0.51 ( 4) hydrogen bonds : bond 0.04571 / 2.95 ( 396) hydrogen bonds : angle 4.74396 / 3.34 ( 1161) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8439 (m110) cc_final: 0.7745 (m110) REVERT: R 108 ARG cc_start: 0.8499 (mtp85) cc_final: 0.8241 (mtp85) REVERT: R 178 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: R 275 PHE cc_start: 0.8661 (p90) cc_final: 0.8314 (p90) outliers start: 13 outliers final: 10 residues processed: 146 average time/residue: 0.0821 time to fit residues: 16.3242 Evaluate side-chains 138 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 80 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 75 optimal weight: 0.0030 chunk 72 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.152210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120943 restraints weight = 7805.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123816 restraints weight = 6290.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125401 restraints weight = 4911.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125591 restraints weight = 4154.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126486 restraints weight = 3966.991| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7167 Z= 0.119 Angle : 0.505 6.190 9710 Z= 0.274 Chirality : 0.041 0.166 1125 Planarity : 0.004 0.062 1213 Dihedral : 4.307 19.125 954 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.23 % Allowed : 10.25 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.29), residues: 876 helix: 1.80 (0.26), residues: 415 sheet: -0.31 (0.38), residues: 169 loop : -1.92 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.010 0.001 TYR R 115 PHE 0.033 0.001 PHE R 275 TRP 0.022 0.002 TRP R 188 HIS 0.002 0.000 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 7165) covalent geometry : angle 0.50523 / 0.27 ( 9706) SS BOND : bond 0.00103 / 0.05 ( 2) SS BOND : angle 0.59006 / 0.37 ( 4) hydrogen bonds : bond 0.03831 / 2.47 ( 396) hydrogen bonds : angle 4.34604 / 3.05 ( 1161) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 THR cc_start: 0.8913 (m) cc_final: 0.8547 (p) REVERT: B 88 ASN cc_start: 0.8367 (m110) cc_final: 0.7795 (m-40) REVERT: R 45 PHE cc_start: 0.6921 (m-80) cc_final: 0.6688 (m-80) REVERT: R 173 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7259 (ttpt) REVERT: R 178 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: R 275 PHE cc_start: 0.8538 (p90) cc_final: 0.8335 (p90) outliers start: 17 outliers final: 11 residues processed: 157 average time/residue: 0.0816 time to fit residues: 17.6331 Evaluate side-chains 134 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 68 optimal weight: 0.0270 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.152374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123077 restraints weight = 7886.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125303 restraints weight = 6044.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127055 restraints weight = 5012.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128077 restraints weight = 4377.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129200 restraints weight = 3974.974| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7167 Z= 0.135 Angle : 0.513 7.431 9710 Z= 0.278 Chirality : 0.042 0.162 1125 Planarity : 0.005 0.090 1213 Dihedral : 4.195 17.293 954 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.50 % Allowed : 12.35 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.29), residues: 876 helix: 1.97 (0.26), residues: 416 sheet: -0.34 (0.38), residues: 172 loop : -1.93 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.011 0.001 TYR R 115 PHE 0.030 0.002 PHE R 275 TRP 0.019 0.002 TRP R 188 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 7165) covalent geometry : angle 0.51318 / 0.28 ( 9706) SS BOND : bond 0.00141 / 0.07 ( 2) SS BOND : angle 0.60831 / 0.37 ( 4) hydrogen bonds : bond 0.03807 / 2.46 ( 396) hydrogen bonds : angle 4.21559 / 2.96 ( 1161) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 ASN cc_start: 0.8390 (m110) cc_final: 0.7818 (m-40) REVERT: B 297 TRP cc_start: 0.8806 (m100) cc_final: 0.8340 (m-10) REVERT: R 173 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7352 (ttpt) REVERT: R 178 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7358 (mt-10) outliers start: 19 outliers final: 17 residues processed: 147 average time/residue: 0.0852 time to fit residues: 17.0015 Evaluate side-chains 145 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 0.0170 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.153375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123907 restraints weight = 7922.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126168 restraints weight = 6037.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127984 restraints weight = 4979.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128765 restraints weight = 4337.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129981 restraints weight = 3996.753| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7167 Z= 0.116 Angle : 0.482 6.117 9710 Z= 0.261 Chirality : 0.041 0.136 1125 Planarity : 0.005 0.095 1213 Dihedral : 4.023 17.350 954 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.02 % Allowed : 12.35 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.29), residues: 876 helix: 2.18 (0.26), residues: 416 sheet: -0.17 (0.38), residues: 174 loop : -1.82 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 108 TYR 0.014 0.001 TYR R 115 PHE 0.023 0.001 PHE R 275 TRP 0.022 0.002 TRP R 188 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 7165) covalent geometry : angle 0.48181 / 0.26 ( 9706) SS BOND : bond 0.00114 / 0.06 ( 2) SS BOND : angle 0.60300 / 0.38 ( 4) hydrogen bonds : bond 0.03563 / 2.30 ( 396) hydrogen bonds : angle 4.06765 / 2.85 ( 1161) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8161 (ttpp) REVERT: B 45 MET cc_start: 0.8442 (mtm) cc_final: 0.8219 (mtm) REVERT: B 88 ASN cc_start: 0.8351 (m110) cc_final: 0.7788 (m-40) REVERT: B 197 ARG cc_start: 0.7470 (mmm160) cc_final: 0.7053 (mmm-85) REVERT: B 297 TRP cc_start: 0.8808 (m100) cc_final: 0.8306 (m-10) REVERT: R 173 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7332 (ttpt) outliers start: 23 outliers final: 18 residues processed: 152 average time/residue: 0.0794 time to fit residues: 16.7074 Evaluate side-chains 156 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 0.0060 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 340 ASN ** 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 = 0.3763 r_free = 0.3763 target = 0.153020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122738 restraints weight = 7886.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125313 restraints weight = 5937.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127082 restraints weight = 4871.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128404 restraints weight = 4229.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129169 restraints weight = 3811.930| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7167 Z= 0.115 Angle : 0.488 9.446 9710 Z= 0.261 Chirality : 0.041 0.132 1125 Planarity : 0.004 0.089 1213 Dihedral : 3.969 16.262 954 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.02 % Allowed : 12.22 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.29), residues: 876 helix: 2.30 (0.26), residues: 416 sheet: -0.23 (0.37), residues: 176 loop : -1.70 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.011 0.001 TYR R 115 PHE 0.034 0.001 PHE R 290 TRP 0.019 0.002 TRP B 169 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7165) covalent geometry : angle 0.48771 / 0.26 ( 9706) SS BOND : bond 0.00120 / 0.06 ( 2) SS BOND : angle 0.55703 / 0.35 ( 4) hydrogen bonds : bond 0.03516 / 2.28 ( 396) hydrogen bonds : angle 4.04973 / 2.84 ( 1161) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LYS cc_start: 0.8360 (pttt) cc_final: 0.8028 (pttm) REVERT: B 45 MET cc_start: 0.8505 (mtm) cc_final: 0.8236 (mtm) REVERT: B 88 ASN cc_start: 0.8381 (m110) cc_final: 0.7778 (m-40) REVERT: B 197 ARG cc_start: 0.7485 (mmm160) cc_final: 0.7083 (mmm-85) REVERT: R 173 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7452 (ttpt) outliers start: 23 outliers final: 19 residues processed: 149 average time/residue: 0.0857 time to fit residues: 17.5577 Evaluate side-chains 151 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.3802 r_free = 0.3802 target = 0.156730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125982 restraints weight = 7653.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126215 restraints weight = 7188.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127305 restraints weight = 6337.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127851 restraints weight = 5633.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128257 restraints weight = 5216.628| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7167 Z= 0.156 Angle : 0.517 8.593 9710 Z= 0.278 Chirality : 0.042 0.135 1125 Planarity : 0.004 0.087 1213 Dihedral : 4.035 16.583 954 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.29 % Allowed : 13.40 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.29), residues: 876 helix: 2.19 (0.26), residues: 416 sheet: -0.13 (0.38), residues: 174 loop : -1.70 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 108 TYR 0.008 0.001 TYR R 115 PHE 0.028 0.002 PHE R 290 TRP 0.020 0.002 TRP R 188 HIS 0.005 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 7165) covalent geometry : angle 0.51727 / 0.28 ( 9706) SS BOND : bond 0.00179 / 0.09 ( 2) SS BOND : angle 0.59115 / 0.35 ( 4) hydrogen bonds : bond 0.03786 / 2.45 ( 396) hydrogen bonds : angle 4.13785 / 2.91 ( 1161) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LYS cc_start: 0.8405 (pttt) cc_final: 0.8076 (pttm) REVERT: B 45 MET cc_start: 0.8560 (mtm) cc_final: 0.8271 (mtm) REVERT: B 88 ASN cc_start: 0.8377 (m110) cc_final: 0.7837 (m-40) REVERT: B 197 ARG cc_start: 0.7458 (mmm160) cc_final: 0.7065 (mmm-85) REVERT: R 144 PHE cc_start: 0.6741 (m-10) cc_final: 0.6530 (m-10) REVERT: R 173 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7530 (ttpt) outliers start: 25 outliers final: 18 residues processed: 154 average time/residue: 0.0781 time to fit residues: 16.4382 Evaluate side-chains 155 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 286 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.3766 r_free = 0.3766 target = 0.153389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.123163 restraints weight = 7863.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125595 restraints weight = 5926.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127504 restraints weight = 4843.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128926 restraints weight = 4231.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129338 restraints weight = 3799.974| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7167 Z= 0.108 Angle : 0.478 8.219 9710 Z= 0.256 Chirality : 0.040 0.141 1125 Planarity : 0.004 0.067 1213 Dihedral : 3.867 15.710 954 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.76 % Allowed : 14.06 % Favored : 83.18 % 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: 0.98 (0.30), residues: 876 helix: 2.43 (0.26), residues: 416 sheet: -0.12 (0.39), residues: 176 loop : -1.61 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 108 TYR 0.011 0.001 TYR R 115 PHE 0.025 0.001 PHE R 290 TRP 0.021 0.002 TRP B 169 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 7165) covalent geometry : angle 0.47841 / 0.26 ( 9706) SS BOND : bond 0.00106 / 0.05 ( 2) SS BOND : angle 0.44012 / 0.27 ( 4) hydrogen bonds : bond 0.03420 / 2.22 ( 396) hydrogen bonds : angle 4.00378 / 2.80 ( 1161) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 LYS cc_start: 0.8417 (pttt) cc_final: 0.8086 (pttm) REVERT: B 45 MET cc_start: 0.8474 (mtm) cc_final: 0.8189 (mtm) REVERT: B 88 ASN cc_start: 0.8340 (m110) cc_final: 0.7767 (m-40) REVERT: B 197 ARG cc_start: 0.7375 (mmm160) cc_final: 0.6997 (mmm-85) REVERT: B 297 TRP cc_start: 0.8786 (m100) cc_final: 0.8316 (m-10) REVERT: R 173 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7588 (ttpt) outliers start: 21 outliers final: 18 residues processed: 151 average time/residue: 0.0832 time to fit residues: 17.1704 Evaluate side-chains 149 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 283 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 53 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.3751 r_free = 0.3751 target = 0.151968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121931 restraints weight = 7844.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124450 restraints weight = 5931.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126076 restraints weight = 4887.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127417 restraints weight = 4255.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.128384 restraints weight = 3864.948| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7167 Z= 0.129 Angle : 0.505 8.266 9710 Z= 0.270 Chirality : 0.041 0.142 1125 Planarity : 0.004 0.044 1213 Dihedral : 3.892 15.845 954 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.76 % Allowed : 14.45 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.29), residues: 876 helix: 2.40 (0.26), residues: 416 sheet: -0.18 (0.38), residues: 173 loop : -1.54 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 108 TYR 0.007 0.001 TYR B 124 PHE 0.024 0.001 PHE R 290 TRP 0.022 0.002 TRP B 169 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7165) covalent geometry : angle 0.50454 / 0.27 ( 9706) SS BOND : bond 0.00135 / 0.07 ( 2) SS BOND : angle 0.50908 / 0.31 ( 4) hydrogen bonds : bond 0.03525 / 2.29 ( 396) hydrogen bonds : angle 3.98120 / 2.81 ( 1161) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8543 (mtm) cc_final: 0.8249 (mtm) REVERT: B 88 ASN cc_start: 0.8344 (m110) cc_final: 0.7790 (m-40) REVERT: B 197 ARG cc_start: 0.7381 (mmm160) cc_final: 0.7004 (mmm-85) REVERT: B 297 TRP cc_start: 0.8829 (m100) cc_final: 0.8316 (m-10) REVERT: R 173 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7664 (ttpt) outliers start: 21 outliers final: 18 residues processed: 150 average time/residue: 0.0829 time to fit residues: 17.1226 Evaluate side-chains 151 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 173 LYS Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 283 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 78 optimal weight: 0.3980 chunk 75 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.3775 r_free = 0.3775 target = 0.154105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124101 restraints weight = 7815.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126704 restraints weight = 5864.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128628 restraints weight = 4790.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129828 restraints weight = 4132.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130777 restraints weight = 3731.877| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7167 Z= 0.108 Angle : 0.485 8.090 9710 Z= 0.260 Chirality : 0.040 0.145 1125 Planarity : 0.004 0.043 1213 Dihedral : 3.802 15.533 954 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.63 % Allowed : 14.32 % Favored : 83.05 % 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: 1.07 (0.30), residues: 876 helix: 2.50 (0.26), residues: 416 sheet: -0.27 (0.38), residues: 175 loop : -1.42 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 108 TYR 0.009 0.001 TYR R 115 PHE 0.022 0.001 PHE R 290 TRP 0.023 0.002 TRP B 169 HIS 0.002 0.000 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7165) covalent geometry : angle 0.48521 / 0.26 ( 9706) SS BOND : bond 0.00093 / 0.05 ( 2) SS BOND : angle 0.43309 / 0.27 ( 4) hydrogen bonds : bond 0.03363 / 2.18 ( 396) hydrogen bonds : angle 3.92956 / 2.77 ( 1161) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 THR cc_start: 0.8723 (m) cc_final: 0.8478 (p) REVERT: B 88 ASN cc_start: 0.8344 (m110) cc_final: 0.7768 (m-40) REVERT: B 197 ARG cc_start: 0.7295 (mmm160) cc_final: 0.6937 (mmm-85) REVERT: B 297 TRP cc_start: 0.8773 (m100) cc_final: 0.8344 (m-10) outliers start: 20 outliers final: 18 residues processed: 151 average time/residue: 0.0882 time to fit residues: 17.9374 Evaluate side-chains 155 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 78 HIS Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 159 ASN Chi-restraints excluded: chain R residue 275 PHE Chi-restraints excluded: chain R residue 281 SER Chi-restraints excluded: chain R residue 283 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.0060 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.3783 r_free = 0.3783 target = 0.154704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124676 restraints weight = 7769.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127194 restraints weight = 5847.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.129209 restraints weight = 4789.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130418 restraints weight = 4135.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130872 restraints weight = 3740.486| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7167 Z= 0.107 Angle : 0.488 8.068 9710 Z= 0.262 Chirality : 0.040 0.184 1125 Planarity : 0.004 0.043 1213 Dihedral : 3.783 16.130 954 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.76 % Allowed : 14.45 % Favored : 82.79 % 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: 1.13 (0.30), residues: 876 helix: 2.51 (0.26), residues: 417 sheet: -0.25 (0.38), residues: 175 loop : -1.34 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 52 TYR 0.007 0.001 TYR B 124 PHE 0.022 0.001 PHE R 290 TRP 0.025 0.002 TRP B 169 HIS 0.002 0.000 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 7165) covalent geometry : angle 0.48821 / 0.26 ( 9706) SS BOND : bond 0.00077 / 0.04 ( 2) SS BOND : angle 0.44377 / 0.28 ( 4) hydrogen bonds : bond 0.03372 / 2.19 ( 396) hydrogen bonds : angle 3.91095 / 2.75 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1295.79 seconds wall clock time: 23 minutes 13.01 seconds (1393.01 seconds total)