Starting phenix.real_space_refine on Sun Apr 5 09:38:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m7u_63693/04_2026/9m7u_63693.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m7u_63693/04_2026/9m7u_63693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m7u_63693/04_2026/9m7u_63693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m7u_63693/04_2026/9m7u_63693.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m7u_63693/04_2026/9m7u_63693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m7u_63693/04_2026/9m7u_63693.map" } resolution = 3.18 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= -0.002 sd= 0.073 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: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 78 5.16 5 C 5934 2.51 5 N 1508 2.21 5 O 1805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9399 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2602 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain: "G" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1593 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 28, 'rna3p_pyr': 30} Link IDs: {'rna2p': 16, 'rna3p': 58} Chain: "B" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2602 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain: "C" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2602 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Time building chain proxies: 2.36, per 1000 atoms: 0.25 Number of scatterers: 9399 At special positions: 0 Unit cell: (96.5367, 106.103, 109.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 74 15.00 O 1805 8.00 N 1508 7.00 C 5934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.82 Conformation dependent library (CDL) restraints added in 403.5 milliseconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 0 sheets defined 85.3% alpha, 0.0% beta 22 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 31 through 41 Processing helix chain 'A' and resid 46 through 63 Processing helix chain 'A' and resid 67 through 74 removed outlier: 4.325A pdb=" N SER A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 107 removed outlier: 4.562A pdb=" N SER A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 117 Processing helix chain 'A' and resid 117 through 122 removed outlier: 4.526A pdb=" N ASN A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 145 through 167 removed outlier: 3.684A pdb=" N TRP A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Proline residue: A 158 - end of helix removed outlier: 3.775A pdb=" N TYR A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.650A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 186 Processing helix chain 'A' and resid 187 through 203 Processing helix chain 'A' and resid 205 through 231 Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.739A pdb=" N ILE A 244 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 264 Proline residue: A 252 - end of helix removed outlier: 3.606A pdb=" N LEU A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 287 removed outlier: 3.661A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 305 through 324 removed outlier: 4.100A pdb=" N LEU A 309 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 353 Processing helix chain 'B' and resid 32 through 41 removed outlier: 3.701A pdb=" N SER B 40 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 63 removed outlier: 4.382A pdb=" N SER B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 74 removed outlier: 3.805A pdb=" N SER B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 107 removed outlier: 4.566A pdb=" N SER B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 117 removed outlier: 3.775A pdb=" N GLU B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 124 removed outlier: 3.756A pdb=" N LEU B 124 " --> pdb=" O VAL B 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 124' Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.705A pdb=" N MET B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 167 removed outlier: 3.531A pdb=" N TRP B 153 " --> pdb=" O GLN B 149 " (cutoff:3.500A) Proline residue: B 158 - end of helix removed outlier: 3.709A pdb=" N TYR B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.574A pdb=" N MET B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 204 Processing helix chain 'B' and resid 205 through 231 Processing helix chain 'B' and resid 242 through 245 Processing helix chain 'B' and resid 246 through 264 Proline residue: B 252 - end of helix removed outlier: 3.774A pdb=" N LEU B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 286 Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.579A pdb=" N TRP B 303 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 325 through 353 Processing helix chain 'C' and resid 32 through 41 Processing helix chain 'C' and resid 45 through 63 removed outlier: 4.332A pdb=" N SER C 49 " --> pdb=" O TYR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 74 removed outlier: 4.020A pdb=" N HIS C 72 " --> pdb=" O PRO C 68 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET C 73 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 107 Processing helix chain 'C' and resid 107 through 117 Processing helix chain 'C' and resid 117 through 122 removed outlier: 4.373A pdb=" N ASN C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 145 through 167 Proline residue: C 158 - end of helix removed outlier: 3.554A pdb=" N TYR C 167 " --> pdb=" O ASP C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 183 removed outlier: 4.238A pdb=" N SER C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 186 No H-bonds generated for 'chain 'C' and resid 184 through 186' Processing helix chain 'C' and resid 187 through 203 removed outlier: 3.700A pdb=" N MET C 203 " --> pdb=" O GLY C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 231 Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 246 through 264 Proline residue: C 252 - end of helix Processing helix chain 'C' and resid 267 through 286 Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 299 through 304 removed outlier: 3.681A pdb=" N ALA C 304 " --> pdb=" O ALA C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 324 removed outlier: 3.903A pdb=" N LEU C 309 " --> pdb=" O TYR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 353 568 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1240 1.32 - 1.44: 3274 1.44 - 1.57: 5024 1.57 - 1.69: 148 1.69 - 1.81: 135 Bond restraints: 9821 Sorted by residual: bond pdb=" C ALA B 320 " pdb=" N GLN B 321 " ideal model delta sigma weight residual 1.335 1.285 0.050 1.36e-02 5.41e+03 1.34e+01 bond pdb=" C GLN B 321 " pdb=" O GLN B 321 " ideal model delta sigma weight residual 1.237 1.194 0.042 1.19e-02 7.06e+03 1.26e+01 bond pdb=" C ASN B 183 " pdb=" N PRO B 184 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.40e+00 bond pdb=" C GLN B 321 " pdb=" N GLU B 322 " ideal model delta sigma weight residual 1.334 1.316 0.018 1.23e-02 6.61e+03 2.19e+00 bond pdb=" N MET C 140 " pdb=" CA MET C 140 " ideal model delta sigma weight residual 1.456 1.473 -0.018 1.26e-02 6.30e+03 2.02e+00 ... (remaining 9816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 13280 1.69 - 3.39: 341 3.39 - 5.08: 64 5.08 - 6.77: 12 6.77 - 8.47: 2 Bond angle restraints: 13699 Sorted by residual: angle pdb=" N MET B 140 " pdb=" CA MET B 140 " pdb=" C MET B 140 " ideal model delta sigma weight residual 112.45 119.52 -7.07 1.39e+00 5.18e-01 2.59e+01 angle pdb=" N MET C 140 " pdb=" CA MET C 140 " pdb=" C MET C 140 " ideal model delta sigma weight residual 112.92 118.27 -5.35 1.23e+00 6.61e-01 1.89e+01 angle pdb=" N MET B 141 " pdb=" CA MET B 141 " pdb=" C MET B 141 " ideal model delta sigma weight residual 110.14 116.75 -6.61 1.55e+00 4.16e-01 1.82e+01 angle pdb=" C TYR B 125 " pdb=" N ALA B 126 " pdb=" CA ALA B 126 " ideal model delta sigma weight residual 120.09 124.89 -4.80 1.25e+00 6.40e-01 1.48e+01 angle pdb=" N GLN B 321 " pdb=" CA GLN B 321 " pdb=" C GLN B 321 " ideal model delta sigma weight residual 111.36 107.30 4.06 1.09e+00 8.42e-01 1.39e+01 ... (remaining 13694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 5584 34.64 - 69.29: 280 69.29 - 103.93: 30 103.93 - 138.57: 1 138.57 - 173.22: 3 Dihedral angle restraints: 5898 sinusoidal: 2994 harmonic: 2904 Sorted by residual: dihedral pdb=" O4' C G 74 " pdb=" C1' C G 74 " pdb=" N1 C G 74 " pdb=" C2 C G 74 " ideal model delta sinusoidal sigma weight residual -128.00 45.22 -173.22 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA TRP A 170 " pdb=" C TRP A 170 " pdb=" N PHE A 171 " pdb=" CA PHE A 171 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" C4' A G 57 " pdb=" C3' A G 57 " pdb=" O3' A G 57 " pdb=" P U G 58 " ideal model delta sinusoidal sigma weight residual -140.00 32.01 -172.01 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 5895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1353 0.048 - 0.096: 227 0.096 - 0.144: 29 0.144 - 0.192: 5 0.192 - 0.240: 2 Chirality restraints: 1616 Sorted by residual: chirality pdb=" CA MET B 141 " pdb=" N MET B 141 " pdb=" C MET B 141 " pdb=" CB MET B 141 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA MET B 140 " pdb=" N MET B 140 " pdb=" C MET B 140 " pdb=" CB MET B 140 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA PHE C 307 " pdb=" N PHE C 307 " pdb=" C PHE C 307 " pdb=" CB PHE C 307 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.56e-01 ... (remaining 1613 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 325 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO C 326 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 326 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 326 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 126 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A 127 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 126 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO B 127 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 127 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 127 " 0.030 5.00e-02 4.00e+02 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 960 2.74 - 3.28: 9324 3.28 - 3.82: 16563 3.82 - 4.36: 19581 4.36 - 4.90: 32473 Nonbonded interactions: 78901 Sorted by model distance: nonbonded pdb=" O4 U G 13 " pdb=" O6 G G 22 " model vdw 2.201 2.432 nonbonded pdb=" OG SER C 256 " pdb=" OD2 ASP C 315 " model vdw 2.214 3.040 nonbonded pdb=" O2' C G 47 " pdb=" O2' U G 58 " model vdw 2.247 3.040 nonbonded pdb=" O2' G G 15 " pdb=" OP1 U G 16 " model vdw 2.254 3.040 nonbonded pdb=" O2' C G 27 " pdb=" O ASN C 235 " model vdw 2.272 3.040 ... (remaining 78896 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.140 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9821 Z= 0.174 Angle : 0.646 8.468 13699 Z= 0.360 Chirality : 0.037 0.240 1616 Planarity : 0.006 0.064 1392 Dihedral : 19.003 173.216 4008 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 1.80 (0.28), residues: 975 helix: 1.72 (0.20), residues: 747 sheet: None (None), residues: 0 loop : -0.51 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 39 TYR 0.013 0.002 TYR B 118 PHE 0.021 0.001 PHE C 307 TRP 0.013 0.002 TRP B 153 HIS 0.003 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9821) covalent geometry : angle 0.64621 (13699) hydrogen bonds : bond 0.15319 ( 626) hydrogen bonds : angle 5.08422 ( 1744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.322 Fit side-chains REVERT: A 70 MET cc_start: 0.4624 (ttt) cc_final: 0.4070 (tpt) REVERT: A 212 MET cc_start: 0.8176 (mtt) cc_final: 0.7768 (mtt) REVERT: C 112 LYS cc_start: 0.7603 (mtmt) cc_final: 0.7378 (mttp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.0886 time to fit residues: 24.6861 Evaluate side-chains 159 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 187 GLN A 321 GLN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN C 149 GLN C 321 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.216499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139516 restraints weight = 9645.554| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.18 r_work: 0.3429 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9821 Z= 0.194 Angle : 0.629 9.628 13699 Z= 0.314 Chirality : 0.038 0.214 1616 Planarity : 0.006 0.058 1392 Dihedral : 19.961 169.978 2235 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.65 % Allowed : 7.07 % Favored : 91.28 % 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: 2.10 (0.27), residues: 975 helix: 1.96 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.41 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 297 TYR 0.017 0.002 TYR B 167 PHE 0.025 0.002 PHE C 307 TRP 0.019 0.002 TRP A 302 HIS 0.003 0.001 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 9821) covalent geometry : angle 0.62907 (13699) hydrogen bonds : bond 0.04672 ( 626) hydrogen bonds : angle 3.87785 ( 1744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.3795 (ttt) cc_final: 0.3393 (tpt) REVERT: A 144 ASN cc_start: 0.8746 (m110) cc_final: 0.8400 (p0) REVERT: A 212 MET cc_start: 0.8251 (mtt) cc_final: 0.7750 (mtt) REVERT: B 240 LYS cc_start: 0.8093 (pttp) cc_final: 0.7613 (ptpt) REVERT: C 80 MET cc_start: 0.7893 (mmt) cc_final: 0.7583 (mmt) REVERT: C 84 LEU cc_start: 0.8674 (tp) cc_final: 0.8421 (mm) outliers start: 14 outliers final: 6 residues processed: 184 average time/residue: 0.0950 time to fit residues: 24.3469 Evaluate side-chains 159 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 76 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN C 42 HIS C 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.216127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138483 restraints weight = 9515.623| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.12 r_work: 0.3412 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9821 Z= 0.146 Angle : 0.559 13.217 13699 Z= 0.274 Chirality : 0.035 0.189 1616 Planarity : 0.005 0.054 1392 Dihedral : 19.820 169.994 2235 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.65 % Allowed : 9.89 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.28), residues: 975 helix: 2.05 (0.19), residues: 771 sheet: None (None), residues: 0 loop : -0.78 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 297 TYR 0.011 0.002 TYR A 100 PHE 0.024 0.001 PHE C 307 TRP 0.019 0.001 TRP C 59 HIS 0.002 0.001 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9821) covalent geometry : angle 0.55869 (13699) hydrogen bonds : bond 0.04198 ( 626) hydrogen bonds : angle 3.66798 ( 1744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.3961 (ttt) cc_final: 0.3627 (tpt) REVERT: A 144 ASN cc_start: 0.8706 (m110) cc_final: 0.8417 (p0) REVERT: A 167 TYR cc_start: 0.7222 (p90) cc_final: 0.6742 (p90) REVERT: A 212 MET cc_start: 0.8216 (mtt) cc_final: 0.7720 (mtt) REVERT: B 282 MET cc_start: 0.7139 (mmt) cc_final: 0.6536 (mmt) REVERT: B 346 MET cc_start: 0.7244 (mmm) cc_final: 0.6869 (mmm) REVERT: C 322 GLU cc_start: 0.8385 (tp30) cc_final: 0.8097 (tp30) outliers start: 14 outliers final: 6 residues processed: 173 average time/residue: 0.0873 time to fit residues: 21.5321 Evaluate side-chains 165 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.0370 chunk 34 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 97 optimal weight: 0.0670 chunk 37 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.210255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.131593 restraints weight = 9642.789| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.26 r_work: 0.3336 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9821 Z= 0.241 Angle : 0.642 13.945 13699 Z= 0.320 Chirality : 0.040 0.234 1616 Planarity : 0.005 0.051 1392 Dihedral : 19.839 169.352 2235 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.88 % Allowed : 12.72 % Favored : 85.39 % 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: 1.79 (0.27), residues: 975 helix: 1.77 (0.19), residues: 753 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 198 TYR 0.020 0.002 TYR B 167 PHE 0.030 0.002 PHE C 307 TRP 0.022 0.002 TRP C 59 HIS 0.004 0.001 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 9821) covalent geometry : angle 0.64210 (13699) hydrogen bonds : bond 0.04945 ( 626) hydrogen bonds : angle 3.84501 ( 1744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.4044 (ttt) cc_final: 0.3653 (tpt) REVERT: A 144 ASN cc_start: 0.8715 (m110) cc_final: 0.8431 (p0) REVERT: A 163 ASP cc_start: 0.8777 (m-30) cc_final: 0.8547 (m-30) REVERT: A 167 TYR cc_start: 0.7187 (p90) cc_final: 0.6630 (p90) REVERT: A 212 MET cc_start: 0.8208 (mtt) cc_final: 0.7786 (mtt) REVERT: A 334 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8421 (pt) REVERT: B 50 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8425 (tt) REVERT: B 240 LYS cc_start: 0.8409 (pttp) cc_final: 0.8008 (ptpt) REVERT: B 282 MET cc_start: 0.7326 (mmt) cc_final: 0.6755 (mmt) REVERT: B 287 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7497 (mmm-85) REVERT: B 332 MET cc_start: 0.7383 (tmm) cc_final: 0.7056 (tmm) REVERT: B 346 MET cc_start: 0.7546 (mmm) cc_final: 0.7149 (mmm) outliers start: 16 outliers final: 9 residues processed: 175 average time/residue: 0.0929 time to fit residues: 23.2020 Evaluate side-chains 163 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 35 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.214761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136954 restraints weight = 9585.073| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.11 r_work: 0.3394 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9821 Z= 0.123 Angle : 0.546 15.458 13699 Z= 0.267 Chirality : 0.034 0.173 1616 Planarity : 0.005 0.048 1392 Dihedral : 19.691 169.592 2235 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.00 % Allowed : 13.90 % Favored : 84.10 % 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: 2.71 (0.28), residues: 975 helix: 2.44 (0.20), residues: 738 sheet: None (None), residues: 0 loop : -0.29 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 297 TYR 0.014 0.001 TYR A 167 PHE 0.023 0.001 PHE A 107 TRP 0.020 0.001 TRP C 59 HIS 0.002 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9821) covalent geometry : angle 0.54635 (13699) hydrogen bonds : bond 0.03862 ( 626) hydrogen bonds : angle 3.54441 ( 1744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.4023 (ttt) cc_final: 0.3692 (tpt) REVERT: A 100 TYR cc_start: 0.7876 (t80) cc_final: 0.7637 (t80) REVERT: A 144 ASN cc_start: 0.8674 (m110) cc_final: 0.8465 (p0) REVERT: A 212 MET cc_start: 0.8235 (mtt) cc_final: 0.7734 (mtt) REVERT: B 180 MET cc_start: 0.5024 (OUTLIER) cc_final: 0.4652 (tpp) REVERT: B 282 MET cc_start: 0.7367 (mmt) cc_final: 0.6802 (mmt) REVERT: B 287 ARG cc_start: 0.7719 (mmm-85) cc_final: 0.7452 (mmm160) REVERT: B 293 LYS cc_start: 0.7206 (tmtt) cc_final: 0.6974 (ttpt) REVERT: B 346 MET cc_start: 0.7663 (mmm) cc_final: 0.7333 (mmm) REVERT: C 228 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.6689 (m-10) REVERT: C 346 MET cc_start: 0.8012 (mmm) cc_final: 0.7553 (mmp) outliers start: 17 outliers final: 7 residues processed: 162 average time/residue: 0.0908 time to fit residues: 21.2611 Evaluate side-chains 162 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 CYS Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 265 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 91 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 0.0980 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.213805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135454 restraints weight = 9574.267| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.16 r_work: 0.3382 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9821 Z= 0.133 Angle : 0.546 16.347 13699 Z= 0.265 Chirality : 0.035 0.186 1616 Planarity : 0.005 0.047 1392 Dihedral : 19.635 170.227 2235 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.88 % Allowed : 14.72 % Favored : 83.39 % 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: 2.60 (0.27), residues: 975 helix: 2.37 (0.19), residues: 753 sheet: None (None), residues: 0 loop : -0.59 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 230 TYR 0.013 0.001 TYR A 167 PHE 0.023 0.001 PHE A 107 TRP 0.019 0.001 TRP C 59 HIS 0.002 0.001 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9821) covalent geometry : angle 0.54581 (13699) hydrogen bonds : bond 0.03930 ( 626) hydrogen bonds : angle 3.48012 ( 1744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.3936 (ttt) cc_final: 0.3602 (tpt) REVERT: A 144 ASN cc_start: 0.8652 (m110) cc_final: 0.8447 (p0) REVERT: A 212 MET cc_start: 0.8159 (mtt) cc_final: 0.7674 (mtt) REVERT: A 302 TRP cc_start: 0.8803 (m-10) cc_final: 0.8310 (m-10) REVERT: B 180 MET cc_start: 0.4960 (OUTLIER) cc_final: 0.4577 (tpp) REVERT: B 282 MET cc_start: 0.7327 (mmt) cc_final: 0.6750 (mmt) REVERT: B 346 MET cc_start: 0.7618 (mmm) cc_final: 0.7313 (mmm) REVERT: C 227 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6366 (mp) REVERT: C 228 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6735 (m-10) REVERT: C 346 MET cc_start: 0.7840 (mmm) cc_final: 0.7450 (mmp) outliers start: 16 outliers final: 10 residues processed: 162 average time/residue: 0.0933 time to fit residues: 21.7349 Evaluate side-chains 159 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 263 CYS Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 265 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 30.0000 chunk 67 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 HIS ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.212101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.133655 restraints weight = 9539.625| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.13 r_work: 0.3357 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9821 Z= 0.157 Angle : 0.571 16.702 13699 Z= 0.279 Chirality : 0.036 0.195 1616 Planarity : 0.005 0.048 1392 Dihedral : 19.619 170.048 2235 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.00 % Allowed : 15.43 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.27), residues: 975 helix: 2.22 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.48 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.015 0.002 TYR B 167 PHE 0.024 0.001 PHE A 107 TRP 0.022 0.001 TRP C 59 HIS 0.009 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9821) covalent geometry : angle 0.57081 (13699) hydrogen bonds : bond 0.04235 ( 626) hydrogen bonds : angle 3.53589 ( 1744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.304 Fit side-chains REVERT: A 70 MET cc_start: 0.3941 (ttt) cc_final: 0.3593 (tpt) REVERT: A 144 ASN cc_start: 0.8649 (m110) cc_final: 0.8429 (p0) REVERT: A 212 MET cc_start: 0.8196 (mtt) cc_final: 0.7758 (mtt) REVERT: A 302 TRP cc_start: 0.8806 (m-10) cc_final: 0.8310 (m-10) REVERT: B 180 MET cc_start: 0.5095 (OUTLIER) cc_final: 0.4875 (tpp) REVERT: B 282 MET cc_start: 0.7446 (mmt) cc_final: 0.6872 (mmt) REVERT: C 73 MET cc_start: 0.4297 (tpt) cc_final: 0.3987 (tmm) REVERT: C 134 MET cc_start: 0.8901 (ttm) cc_final: 0.8605 (mtt) REVERT: C 227 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6425 (mp) REVERT: C 228 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6735 (m-10) REVERT: C 254 MET cc_start: 0.8241 (tpp) cc_final: 0.6989 (tpp) REVERT: C 346 MET cc_start: 0.7811 (mmm) cc_final: 0.7471 (mmp) outliers start: 17 outliers final: 9 residues processed: 164 average time/residue: 0.0887 time to fit residues: 21.0254 Evaluate side-chains 161 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 263 CYS Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 265 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 100 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.214260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136212 restraints weight = 9453.831| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.20 r_work: 0.3386 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9821 Z= 0.116 Angle : 0.553 17.247 13699 Z= 0.264 Chirality : 0.034 0.175 1616 Planarity : 0.005 0.048 1392 Dihedral : 19.554 170.217 2235 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.65 % Allowed : 16.02 % Favored : 82.33 % 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: 2.93 (0.28), residues: 975 helix: 2.61 (0.19), residues: 735 sheet: None (None), residues: 0 loop : -0.21 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 39 TYR 0.012 0.001 TYR A 167 PHE 0.026 0.001 PHE A 107 TRP 0.020 0.001 TRP C 59 HIS 0.002 0.000 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9821) covalent geometry : angle 0.55263 (13699) hydrogen bonds : bond 0.03772 ( 626) hydrogen bonds : angle 3.44740 ( 1744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.343 Fit side-chains REVERT: A 212 MET cc_start: 0.8146 (mtt) cc_final: 0.7626 (mtt) REVERT: A 302 TRP cc_start: 0.8817 (m-10) cc_final: 0.8340 (m-10) REVERT: B 80 MET cc_start: 0.7876 (mmp) cc_final: 0.7576 (mmm) REVERT: B 282 MET cc_start: 0.7415 (mmt) cc_final: 0.6867 (mmt) REVERT: C 73 MET cc_start: 0.4262 (tpt) cc_final: 0.3951 (tmm) REVERT: C 134 MET cc_start: 0.8892 (ttm) cc_final: 0.8627 (mtt) REVERT: C 227 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6401 (mp) REVERT: C 228 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6695 (m-10) REVERT: C 254 MET cc_start: 0.8287 (tpp) cc_final: 0.6928 (tpp) REVERT: C 346 MET cc_start: 0.7833 (mmm) cc_final: 0.7509 (mmp) outliers start: 14 outliers final: 7 residues processed: 157 average time/residue: 0.0932 time to fit residues: 20.8569 Evaluate side-chains 156 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 263 CYS Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 265 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 56 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.213741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.135783 restraints weight = 9506.796| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.18 r_work: 0.3390 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9821 Z= 0.127 Angle : 0.576 17.802 13699 Z= 0.274 Chirality : 0.035 0.223 1616 Planarity : 0.005 0.048 1392 Dihedral : 19.526 170.416 2235 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.53 % Allowed : 16.84 % Favored : 81.63 % 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: 2.66 (0.27), residues: 975 helix: 2.42 (0.19), residues: 747 sheet: None (None), residues: 0 loop : -0.52 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 287 TYR 0.012 0.001 TYR A 167 PHE 0.026 0.001 PHE A 107 TRP 0.020 0.001 TRP C 59 HIS 0.002 0.000 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9821) covalent geometry : angle 0.57573 (13699) hydrogen bonds : bond 0.03839 ( 626) hydrogen bonds : angle 3.45705 ( 1744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.348 Fit side-chains REVERT: A 70 MET cc_start: 0.4194 (ttp) cc_final: 0.2921 (tpt) REVERT: A 80 MET cc_start: 0.7163 (mmm) cc_final: 0.6834 (mmm) REVERT: A 212 MET cc_start: 0.8090 (mtt) cc_final: 0.7600 (mtt) REVERT: A 302 TRP cc_start: 0.8798 (m-10) cc_final: 0.8295 (m-10) REVERT: B 80 MET cc_start: 0.7790 (mmp) cc_final: 0.7496 (mmm) REVERT: B 282 MET cc_start: 0.7319 (mmt) cc_final: 0.6771 (mmt) REVERT: C 73 MET cc_start: 0.4346 (tpt) cc_final: 0.3992 (tmm) REVERT: C 134 MET cc_start: 0.8875 (ttm) cc_final: 0.8592 (mtt) REVERT: C 227 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6397 (mp) REVERT: C 228 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6777 (m-10) REVERT: C 254 MET cc_start: 0.8223 (tpp) cc_final: 0.6892 (tpp) REVERT: C 346 MET cc_start: 0.7751 (mmm) cc_final: 0.7451 (mmp) outliers start: 13 outliers final: 8 residues processed: 157 average time/residue: 0.0973 time to fit residues: 21.7825 Evaluate side-chains 156 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 263 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.0070 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 30.0000 chunk 87 optimal weight: 0.6980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.215382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136086 restraints weight = 9474.567| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.21 r_work: 0.3395 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9821 Z= 0.113 Angle : 0.572 18.030 13699 Z= 0.269 Chirality : 0.035 0.330 1616 Planarity : 0.005 0.048 1392 Dihedral : 19.463 170.464 2235 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.53 % Allowed : 16.84 % Favored : 81.63 % 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: 3.06 (0.28), residues: 975 helix: 2.69 (0.19), residues: 735 sheet: None (None), residues: 0 loop : -0.15 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 287 TYR 0.011 0.001 TYR A 167 PHE 0.025 0.001 PHE A 107 TRP 0.018 0.001 TRP C 59 HIS 0.002 0.000 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9821) covalent geometry : angle 0.57220 (13699) hydrogen bonds : bond 0.03580 ( 626) hydrogen bonds : angle 3.41976 ( 1744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.4482 (ttp) cc_final: 0.3481 (tpt) REVERT: A 80 MET cc_start: 0.7116 (mmm) cc_final: 0.6785 (mmm) REVERT: A 212 MET cc_start: 0.8112 (mtt) cc_final: 0.7580 (mtt) REVERT: A 302 TRP cc_start: 0.8811 (m-10) cc_final: 0.8319 (m-10) REVERT: B 282 MET cc_start: 0.7405 (mmt) cc_final: 0.6877 (mmt) REVERT: B 332 MET cc_start: 0.7494 (tmm) cc_final: 0.7180 (tmm) REVERT: C 73 MET cc_start: 0.4250 (tpt) cc_final: 0.3928 (tmm) REVERT: C 87 TYR cc_start: 0.7768 (m-80) cc_final: 0.7447 (m-80) REVERT: C 134 MET cc_start: 0.8785 (ttm) cc_final: 0.8512 (mtt) REVERT: C 227 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6403 (mp) REVERT: C 228 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.6781 (m-10) REVERT: C 254 MET cc_start: 0.8266 (tpp) cc_final: 0.6887 (tpp) outliers start: 13 outliers final: 11 residues processed: 164 average time/residue: 0.0920 time to fit residues: 21.7439 Evaluate side-chains 162 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 263 CYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 77 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 30.0000 chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.214416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.136861 restraints weight = 9414.651| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.20 r_work: 0.3388 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9821 Z= 0.121 Angle : 0.592 18.130 13699 Z= 0.275 Chirality : 0.036 0.318 1616 Planarity : 0.005 0.048 1392 Dihedral : 19.440 170.378 2235 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.65 % Allowed : 16.96 % Favored : 81.39 % 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: 3.03 (0.27), residues: 975 helix: 2.67 (0.19), residues: 735 sheet: None (None), residues: 0 loop : -0.17 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 287 TYR 0.011 0.001 TYR A 167 PHE 0.025 0.001 PHE A 107 TRP 0.022 0.001 TRP C 59 HIS 0.002 0.000 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9821) covalent geometry : angle 0.59242 (13699) hydrogen bonds : bond 0.03689 ( 626) hydrogen bonds : angle 3.44743 ( 1744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.28 seconds wall clock time: 53 minutes 35.25 seconds (3215.25 seconds total)