Starting phenix.real_space_refine on Fri Jul 25 02:36:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d9h_7835/07_2025/6d9h_7835.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d9h_7835/07_2025/6d9h_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_7835/07_2025/6d9h_7835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d9h_7835/07_2025/6d9h_7835.map" model { file = "/net/cci-nas-00/data/ceres_data/6d9h_7835/07_2025/6d9h_7835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d9h_7835/07_2025/6d9h_7835.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.37, per 1000 atoms: 0.76 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: 2.56 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.07 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: 1.78 Time building geometry restraints manager: 2.62 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: 9280 1.97 - 3.94: 352 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: 4095 15.22 - 30.44: 145 30.44 - 45.66: 43 45.66 - 60.88: 6 60.88 - 76.10: 4 Dihedral angle restraints: 4293 sinusoidal: 1691 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 4290 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.180 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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= 0.273 Angle : 0.933 9.857 9710 Z= 0.518 Chirality : 0.056 0.291 1125 Planarity : 0.007 0.050 1213 Dihedral : 9.573 76.099 2595 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.18 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.049 0.004 TRP R 146 HIS 0.007 0.002 HIS B 311 PHE 0.039 0.004 PHE R 171 TYR 0.021 0.003 TYR R 179 ARG 0.008 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.11970 ( 396) hydrogen bonds : angle 5.90794 ( 1161) SS BOND : bond 0.00275 ( 2) SS BOND : angle 1.44368 ( 4) covalent geometry : bond 0.00612 ( 7165) covalent geometry : angle 0.93316 ( 9706) *********************** 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 : 1.037 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: 0.7065 (t0) REVERT: R 89 ILE cc_start: 0.8617 (mt) cc_final: 0.8365 (mt) REVERT: R 117 MET cc_start: 0.7175 (ptm) cc_final: 0.6941 (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: 0.1965 time to fit residues: 49.1698 Evaluate side-chains 127 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS A 295 ASN A 332 ASN B 6 GLN B 88 ASN B 239 ASN B 266 HIS B 340 ASN 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 = 0.3755 r_free = 0.3755 target = 0.153489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122042 restraints weight = 7780.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125305 restraints weight = 6255.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126199 restraints weight = 4645.612| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7167 Z= 0.132 Angle : 0.542 5.736 9710 Z= 0.294 Chirality : 0.042 0.171 1125 Planarity : 0.004 0.045 1213 Dihedral : 5.758 56.550 976 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.18 % Allowed : 9.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.28), residues: 876 helix: 1.37 (0.25), residues: 414 sheet: -0.28 (0.38), residues: 164 loop : -2.16 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 188 HIS 0.002 0.001 HIS B 266 PHE 0.038 0.002 PHE R 275 TYR 0.019 0.001 TYR R 115 ARG 0.007 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 396) hydrogen bonds : angle 4.56744 ( 1161) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.72715 ( 4) covalent geometry : bond 0.00292 ( 7165) covalent geometry : angle 0.54206 ( 9706) *********************** 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 151 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 THR cc_start: 0.8918 (m) cc_final: 0.8551 (p) REVERT: B 88 ASN cc_start: 0.8409 (m110) cc_final: 0.7737 (m110) REVERT: B 98 SER cc_start: 0.8142 (m) cc_final: 0.7810 (t) REVERT: R 178 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: R 275 PHE cc_start: 0.8625 (p90) cc_final: 0.8299 (p90) outliers start: 9 outliers final: 6 residues processed: 146 average time/residue: 0.3260 time to fit residues: 64.4883 Evaluate side-chains 129 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.153678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122743 restraints weight = 7824.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125369 restraints weight = 6709.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126772 restraints weight = 5042.574| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2275 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= 0.120 Angle : 0.510 6.224 9710 Z= 0.275 Chirality : 0.041 0.168 1125 Planarity : 0.004 0.046 1213 Dihedral : 5.361 52.727 976 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.23 % Allowed : 9.86 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.29), residues: 876 helix: 1.86 (0.26), residues: 415 sheet: -0.15 (0.39), residues: 164 loop : -1.89 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 188 HIS 0.002 0.001 HIS R 251 PHE 0.033 0.002 PHE R 275 TYR 0.017 0.001 TYR R 115 ARG 0.003 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 396) hydrogen bonds : angle 4.32792 ( 1161) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.59947 ( 4) covalent geometry : bond 0.00268 ( 7165) covalent geometry : angle 0.51037 ( 9706) *********************** 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 160 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8254 (ttpp) REVERT: A 322 THR cc_start: 0.8912 (m) cc_final: 0.8514 (p) REVERT: A 342 ASP cc_start: 0.8604 (t0) cc_final: 0.8329 (t0) REVERT: B 88 ASN cc_start: 0.8346 (m110) cc_final: 0.7777 (m-40) REVERT: B 297 TRP cc_start: 0.8773 (m100) cc_final: 0.8252 (m-10) REVERT: R 178 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7361 (mt-10) outliers start: 17 outliers final: 12 residues processed: 150 average time/residue: 0.2391 time to fit residues: 48.1374 Evaluate side-chains 133 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 69 LEU 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 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 65 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 38 GLN R 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120772 restraints weight = 7960.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122869 restraints weight = 6712.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123659 restraints weight = 5563.863| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2481 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= 0.130 Angle : 0.502 7.279 9710 Z= 0.271 Chirality : 0.041 0.142 1125 Planarity : 0.004 0.046 1213 Dihedral : 5.218 50.041 976 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.23 % Allowed : 11.56 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 876 helix: 2.04 (0.26), residues: 415 sheet: -0.39 (0.37), residues: 172 loop : -1.74 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 188 HIS 0.002 0.001 HIS A 189 PHE 0.023 0.001 PHE R 275 TYR 0.016 0.001 TYR R 115 ARG 0.002 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 396) hydrogen bonds : angle 4.21017 ( 1161) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.58715 ( 4) covalent geometry : bond 0.00298 ( 7165) covalent geometry : angle 0.50150 ( 9706) *********************** 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 143 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 THR cc_start: 0.8928 (m) cc_final: 0.8544 (p) REVERT: B 88 ASN cc_start: 0.8350 (m110) cc_final: 0.7810 (m-40) REVERT: B 123 ILE cc_start: 0.8703 (mm) cc_final: 0.8452 (mt) REVERT: B 297 TRP cc_start: 0.8795 (m100) cc_final: 0.8311 (m-10) REVERT: R 173 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7348 (ttpt) REVERT: R 178 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7387 (mt-10) outliers start: 17 outliers final: 15 residues processed: 134 average time/residue: 0.2685 time to fit residues: 49.3838 Evaluate side-chains 143 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.801 ------------------------------------------------------------------------------- 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 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 294 CYS Chi-restraints excluded: chain R residue 49 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 68 optimal weight: 0.0770 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.171669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.138219 restraints weight = 7239.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140976 restraints weight = 5495.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143265 restraints weight = 4519.562| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7167 Z= 0.121 Angle : 0.489 6.220 9710 Z= 0.265 Chirality : 0.041 0.151 1125 Planarity : 0.004 0.046 1213 Dihedral : 4.985 47.766 976 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.76 % Allowed : 12.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.29), residues: 876 helix: 2.17 (0.26), residues: 416 sheet: -0.29 (0.37), residues: 170 loop : -1.72 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 188 HIS 0.002 0.001 HIS B 91 PHE 0.021 0.001 PHE R 275 TYR 0.013 0.001 TYR R 115 ARG 0.006 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 396) hydrogen bonds : angle 4.13045 ( 1161) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.60132 ( 4) covalent geometry : bond 0.00277 ( 7165) covalent geometry : angle 0.48873 ( 9706) *********************** 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 160 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8164 (ttpp) REVERT: B 88 ASN cc_start: 0.8346 (m110) cc_final: 0.7805 (m-40) REVERT: B 123 ILE cc_start: 0.8800 (mm) cc_final: 0.8570 (mt) REVERT: R 173 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7213 (ttpt) outliers start: 21 outliers final: 17 residues processed: 149 average time/residue: 0.1984 time to fit residues: 39.7539 Evaluate side-chains 147 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 326 CYS 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 260 GLU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 49 VAL 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 83 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 38 optimal weight: 0.1980 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126913 restraints weight = 7766.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129327 restraints weight = 5879.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131218 restraints weight = 4836.207| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2880 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= 0.102 Angle : 0.479 9.655 9710 Z= 0.255 Chirality : 0.040 0.138 1125 Planarity : 0.004 0.044 1213 Dihedral : 4.835 47.493 976 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.63 % Allowed : 12.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.29), residues: 876 helix: 2.37 (0.26), residues: 417 sheet: -0.19 (0.37), residues: 168 loop : -1.63 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.002 0.000 HIS A 189 PHE 0.019 0.001 PHE R 275 TYR 0.017 0.001 TYR R 115 ARG 0.006 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 396) hydrogen bonds : angle 3.96728 ( 1161) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.51898 ( 4) covalent geometry : bond 0.00222 ( 7165) covalent geometry : angle 0.47893 ( 9706) *********************** 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 165 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.8637 (ptp90) cc_final: 0.8398 (ptp-110) REVERT: B 88 ASN cc_start: 0.8266 (m110) cc_final: 0.7742 (m-40) REVERT: B 297 TRP cc_start: 0.8781 (m100) cc_final: 0.8377 (m-10) REVERT: R 173 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7314 (ttpt) outliers start: 20 outliers final: 16 residues processed: 154 average time/residue: 0.2616 time to fit residues: 55.4673 Evaluate side-chains 150 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 326 CYS 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 294 CYS Chi-restraints excluded: chain R residue 49 VAL 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 28 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123549 restraints weight = 7777.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125889 restraints weight = 5974.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127647 restraints weight = 4954.505| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3005 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= 0.131 Angle : 0.502 8.186 9710 Z= 0.268 Chirality : 0.041 0.135 1125 Planarity : 0.004 0.045 1213 Dihedral : 4.984 50.109 976 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.29 % Allowed : 12.35 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.29), residues: 876 helix: 2.32 (0.26), residues: 417 sheet: -0.09 (0.38), residues: 169 loop : -1.63 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.003 0.001 HIS A 189 PHE 0.017 0.001 PHE R 275 TYR 0.015 0.001 TYR R 115 ARG 0.004 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 396) hydrogen bonds : angle 4.04836 ( 1161) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.54969 ( 4) covalent geometry : bond 0.00306 ( 7165) covalent geometry : angle 0.50182 ( 9706) *********************** 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 157 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.8661 (ptp90) cc_final: 0.8456 (ptp-110) REVERT: B 88 ASN cc_start: 0.8295 (m110) cc_final: 0.7762 (m-40) REVERT: B 297 TRP cc_start: 0.8790 (m100) cc_final: 0.8350 (m-10) REVERT: R 173 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7481 (ttpt) outliers start: 25 outliers final: 18 residues processed: 145 average time/residue: 0.3507 time to fit residues: 70.9251 Evaluate side-chains 158 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 326 CYS 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 276 VAL 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 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 286 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.153428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123959 restraints weight = 7814.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126220 restraints weight = 5988.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127993 restraints weight = 4958.163| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3097 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= 0.125 Angle : 0.494 8.110 9710 Z= 0.264 Chirality : 0.041 0.136 1125 Planarity : 0.004 0.044 1213 Dihedral : 4.964 50.108 976 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.50 % Allowed : 13.27 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.29), residues: 876 helix: 2.36 (0.26), residues: 417 sheet: -0.03 (0.39), residues: 168 loop : -1.55 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 188 HIS 0.002 0.001 HIS R 78 PHE 0.017 0.001 PHE R 275 TYR 0.016 0.001 TYR R 115 ARG 0.004 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 396) hydrogen bonds : angle 4.01068 ( 1161) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.52198 ( 4) covalent geometry : bond 0.00289 ( 7165) covalent geometry : angle 0.49419 ( 9706) *********************** 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 160 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ILE cc_start: 0.7864 (mt) cc_final: 0.7577 (tt) REVERT: B 88 ASN cc_start: 0.8314 (m110) cc_final: 0.7774 (m-40) REVERT: B 297 TRP cc_start: 0.8800 (m100) cc_final: 0.8355 (m-10) REVERT: R 173 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7525 (ttpt) outliers start: 19 outliers final: 18 residues processed: 150 average time/residue: 0.1801 time to fit residues: 36.6180 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 : 0.737 ------------------------------------------------------------------------------- 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 326 CYS 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 276 VAL 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 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 286 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3720 r_free = 0.3720 target = 0.149282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119685 restraints weight = 7999.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121873 restraints weight = 6147.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123601 restraints weight = 5115.391| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7167 Z= 0.182 Angle : 0.557 7.964 9710 Z= 0.298 Chirality : 0.043 0.139 1125 Planarity : 0.004 0.046 1213 Dihedral : 5.334 53.735 976 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.76 % Allowed : 13.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.29), residues: 876 helix: 2.15 (0.26), residues: 416 sheet: -0.34 (0.38), residues: 175 loop : -1.57 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.004 0.001 HIS B 54 PHE 0.039 0.002 PHE R 290 TYR 0.014 0.001 TYR R 115 ARG 0.003 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 396) hydrogen bonds : angle 4.21202 ( 1161) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.66025 ( 4) covalent geometry : bond 0.00435 ( 7165) covalent geometry : angle 0.55657 ( 9706) *********************** 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 163 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8267 (ttmt) cc_final: 0.7924 (tmmt) REVERT: B 88 ASN cc_start: 0.8377 (m110) cc_final: 0.7792 (m-40) REVERT: B 147 SER cc_start: 0.8872 (p) cc_final: 0.8572 (t) REVERT: R 144 PHE cc_start: 0.6873 (m-10) cc_final: 0.6630 (m-10) REVERT: R 173 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7682 (ttpt) outliers start: 21 outliers final: 18 residues processed: 152 average time/residue: 0.2417 time to fit residues: 51.3192 Evaluate side-chains 154 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 326 CYS Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 44 GLN 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 276 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.152779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122710 restraints weight = 7933.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125284 restraints weight = 5964.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127043 restraints weight = 4885.773| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3247 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 7.801 9710 Z= 0.270 Chirality : 0.041 0.145 1125 Planarity : 0.004 0.046 1213 Dihedral : 5.006 49.883 976 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.23 % Allowed : 14.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.30), residues: 876 helix: 2.35 (0.26), residues: 416 sheet: -0.33 (0.38), residues: 175 loop : -1.50 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 188 HIS 0.002 0.001 HIS B 54 PHE 0.031 0.001 PHE R 290 TYR 0.016 0.001 TYR R 115 ARG 0.007 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 396) hydrogen bonds : angle 4.04456 ( 1161) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.46973 ( 4) covalent geometry : bond 0.00270 ( 7165) covalent geometry : angle 0.50497 ( 9706) ********************** 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 150 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.7794 (mmmt) cc_final: 0.7131 (mmtt) REVERT: B 88 ASN cc_start: 0.8338 (m110) cc_final: 0.7793 (m-40) REVERT: B 197 ARG cc_start: 0.7417 (mmm160) cc_final: 0.6528 (mmm160) REVERT: B 297 TRP cc_start: 0.8819 (m100) cc_final: 0.8337 (m100) REVERT: R 144 PHE cc_start: 0.6786 (m-10) cc_final: 0.6582 (m-10) REVERT: R 173 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7656 (ttpt) outliers start: 17 outliers final: 16 residues processed: 142 average time/residue: 0.2610 time to fit residues: 51.7746 Evaluate side-chains 150 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 44 GLN 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 276 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.153429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123967 restraints weight = 7915.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126278 restraints weight = 5984.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.128167 restraints weight = 4920.432| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3314 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= 0.121 Angle : 0.502 7.794 9710 Z= 0.269 Chirality : 0.041 0.182 1125 Planarity : 0.004 0.046 1213 Dihedral : 4.897 47.668 976 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.37 % Allowed : 14.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.30), residues: 876 helix: 2.42 (0.26), residues: 416 sheet: -0.32 (0.38), residues: 176 loop : -1.42 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 188 HIS 0.002 0.000 HIS B 183 PHE 0.031 0.001 PHE R 290 TYR 0.017 0.001 TYR R 115 ARG 0.008 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 396) hydrogen bonds : angle 4.00955 ( 1161) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.51487 ( 4) covalent geometry : bond 0.00277 ( 7165) covalent geometry : angle 0.50219 ( 9706) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3438.02 seconds wall clock time: 65 minutes 44.29 seconds (3944.29 seconds total)