Starting phenix.real_space_refine on Thu Jul 2 17:52:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m7u_63693/07_2026/9m7u_63693.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m7u_63693/07_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_63693/07_2026/9m7u_63693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m7u_63693/07_2026/9m7u_63693.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m7u_63693/07_2026/9m7u_63693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m7u_63693/07_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-dev-6108/lib/python3.11/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: 1.80, per 1000 atoms: 0.19 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: 0.65 Conformation dependent library (CDL) restraints added in 217.1 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: 0.95 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: 1.27 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.060 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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= 0.180 Angle : 0.646 8.468 13699 Z= 0.396 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/Z covalent geometry : bond 0.00375 / 0.18 ( 9821) covalent geometry : angle 0.64627 / 0.40 (13699) hydrogen bonds : bond 0.15319 / 10.39 ( 626) hydrogen bonds : angle 5.08422 / 3.60 ( 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 : 0.303 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: 0.0874 time to fit residues: 24.2566 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 : 0.318 ------------------------------------------------------------------------------- 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: 50.0000 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: 40.0000 chunk 61 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN C 318 GLN C 321 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.219537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.144963 restraints weight = 9710.523| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.06 r_work: 0.3493 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9821 Z= 0.199 Angle : 0.630 10.821 13699 Z= 0.318 Chirality : 0.039 0.218 1616 Planarity : 0.006 0.061 1392 Dihedral : 20.067 173.986 2235 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.71 % Allowed : 8.48 % Favored : 90.81 % 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: 1.93 (0.27), residues: 975 helix: 1.78 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.46 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 230 TYR 0.017 0.002 TYR B 167 PHE 0.026 0.002 PHE C 307 TRP 0.017 0.002 TRP C 153 HIS 0.003 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 9821) covalent geometry : angle 0.63027 / 0.32 (13699) hydrogen bonds : bond 0.05056 / 3.41 ( 626) hydrogen bonds : angle 3.95268 / 2.79 ( 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 171 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 165 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 35 MET cc_start: 0.6452 (mmt) cc_final: 0.6084 (tpp) REVERT: A 70 MET cc_start: 0.3919 (ttt) cc_final: 0.3312 (tpt) REVERT: A 144 ASN cc_start: 0.8688 (m110) cc_final: 0.8238 (p0) REVERT: A 163 ASP cc_start: 0.8375 (m-30) cc_final: 0.8115 (m-30) REVERT: A 180 MET cc_start: 0.8085 (tpp) cc_final: 0.7812 (tpt) REVERT: A 212 MET cc_start: 0.8265 (mtt) cc_final: 0.7766 (mtt) REVERT: A 302 TRP cc_start: 0.8386 (m-10) cc_final: 0.8161 (m-10) REVERT: B 112 LYS cc_start: 0.7920 (ttmm) cc_final: 0.7497 (tptp) REVERT: B 115 PHE cc_start: 0.7612 (t80) cc_final: 0.7374 (t80) REVERT: B 282 MET cc_start: 0.7181 (mmt) cc_final: 0.6723 (mmm) outliers start: 6 outliers final: 5 residues processed: 168 average time/residue: 0.0958 time to fit residues: 22.5921 Evaluate side-chains 162 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 227 LEU 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: 0.7980 chunk 51 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 86 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 GLN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.221771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.144793 restraints weight = 9570.135| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.21 r_work: 0.3475 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9821 Z= 0.115 Angle : 0.537 14.783 13699 Z= 0.266 Chirality : 0.034 0.171 1616 Planarity : 0.005 0.054 1392 Dihedral : 19.964 173.027 2235 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.30 % Allowed : 9.78 % Favored : 88.93 % 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: 2.70 (0.28), residues: 975 helix: 2.45 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.35 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 287 TYR 0.015 0.001 TYR A 167 PHE 0.021 0.001 PHE A 107 TRP 0.018 0.001 TRP C 59 HIS 0.003 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 9821) covalent geometry : angle 0.53742 / 0.27 (13699) hydrogen bonds : bond 0.04298 / 2.92 ( 626) hydrogen bonds : angle 3.69194 / 2.60 ( 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 177 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.3987 (ttt) cc_final: 0.3319 (tpt) REVERT: A 167 TYR cc_start: 0.7252 (p90) cc_final: 0.6925 (p90) REVERT: A 212 MET cc_start: 0.8139 (mtt) cc_final: 0.7626 (mtt) REVERT: B 112 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7538 (tptp) REVERT: B 240 LYS cc_start: 0.7953 (pttp) cc_final: 0.7452 (ptpt) REVERT: C 84 LEU cc_start: 0.8330 (mm) cc_final: 0.8098 (mm) outliers start: 11 outliers final: 5 residues processed: 170 average time/residue: 0.0980 time to fit residues: 23.4893 Evaluate side-chains 158 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 153 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU 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 342 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 30.0000 chunk 4 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 50.0000 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 38 optimal weight: 40.0000 chunk 47 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN C 42 HIS ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.214619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137468 restraints weight = 9639.949| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.12 r_work: 0.3391 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9821 Z= 0.203 Angle : 0.623 14.590 13699 Z= 0.311 Chirality : 0.039 0.224 1616 Planarity : 0.005 0.053 1392 Dihedral : 19.933 173.237 2235 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.88 % Allowed : 10.84 % Favored : 87.28 % 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: 1.99 (0.27), residues: 975 helix: 1.91 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.75 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.016 0.002 TYR A 148 PHE 0.030 0.002 PHE C 307 TRP 0.025 0.002 TRP C 59 HIS 0.004 0.001 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.20 ( 9821) covalent geometry : angle 0.62261 / 0.31 (13699) hydrogen bonds : bond 0.04881 / 3.30 ( 626) hydrogen bonds : angle 3.82325 / 2.73 ( 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 178 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 112 LYS cc_start: 0.5284 (tptt) cc_final: 0.5040 (tptt) REVERT: A 144 ASN cc_start: 0.8720 (m110) cc_final: 0.8391 (p0) REVERT: A 212 MET cc_start: 0.8223 (mtt) cc_final: 0.7747 (mtt) REVERT: A 242 ARG cc_start: 0.8496 (tpt-90) cc_final: 0.8289 (tpp-160) REVERT: B 282 MET cc_start: 0.7157 (mmt) cc_final: 0.6533 (mmt) REVERT: C 80 MET cc_start: 0.7890 (mmt) cc_final: 0.7587 (tpt) REVERT: C 84 LEU cc_start: 0.8632 (mm) cc_final: 0.8291 (mm) REVERT: C 203 MET cc_start: 0.8628 (mtm) cc_final: 0.8413 (mtm) outliers start: 16 outliers final: 9 residues processed: 169 average time/residue: 0.0850 time to fit residues: 20.9792 Evaluate side-chains 164 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 140 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 35 optimal weight: 50.0000 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 50.0000 chunk 88 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.216458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.140163 restraints weight = 9585.809| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.08 r_work: 0.3422 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9821 Z= 0.128 Angle : 0.557 16.274 13699 Z= 0.272 Chirality : 0.036 0.282 1616 Planarity : 0.005 0.049 1392 Dihedral : 19.871 173.208 2235 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.94 % Allowed : 12.84 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.28), residues: 975 helix: 2.11 (0.19), residues: 771 sheet: None (None), residues: 0 loop : -0.83 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 198 TYR 0.015 0.002 TYR A 167 PHE 0.024 0.001 PHE A 107 TRP 0.020 0.001 TRP C 59 HIS 0.002 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9821) covalent geometry : angle 0.55687 / 0.27 (13699) hydrogen bonds : bond 0.04257 / 2.91 ( 626) hydrogen bonds : angle 3.64881 / 2.59 ( 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 175 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 144 ASN cc_start: 0.8689 (m110) cc_final: 0.8360 (p0) REVERT: A 212 MET cc_start: 0.8200 (mtt) cc_final: 0.7696 (mtt) REVERT: B 112 LYS cc_start: 0.7852 (ttmm) cc_final: 0.7370 (tptp) REVERT: B 240 LYS cc_start: 0.8310 (pttp) cc_final: 0.7846 (ptpt) REVERT: B 282 MET cc_start: 0.7207 (mmt) cc_final: 0.6619 (mmt) REVERT: C 80 MET cc_start: 0.7745 (mmt) cc_final: 0.7463 (mmt) REVERT: C 84 LEU cc_start: 0.8720 (mm) cc_final: 0.8372 (mm) REVERT: C 203 MET cc_start: 0.8599 (mtm) cc_final: 0.8363 (mtm) REVERT: C 228 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6558 (m-80) outliers start: 8 outliers final: 6 residues processed: 171 average time/residue: 0.0937 time to fit residues: 22.7743 Evaluate side-chains 170 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 227 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.216267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137881 restraints weight = 9584.737| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.21 r_work: 0.3418 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9821 Z= 0.124 Angle : 0.538 16.741 13699 Z= 0.263 Chirality : 0.035 0.177 1616 Planarity : 0.005 0.048 1392 Dihedral : 19.807 173.482 2235 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.53 % Allowed : 13.43 % Favored : 85.04 % 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: 2.65 (0.28), residues: 975 helix: 2.38 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.54 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.010 0.001 TYR A 319 PHE 0.024 0.001 PHE A 107 TRP 0.021 0.001 TRP C 59 HIS 0.002 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 9821) covalent geometry : angle 0.53772 / 0.26 (13699) hydrogen bonds : bond 0.04080 / 2.78 ( 626) hydrogen bonds : angle 3.58779 / 2.54 ( 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 183 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7603 (tpt) REVERT: A 212 MET cc_start: 0.8174 (mtt) cc_final: 0.7668 (mtt) REVERT: A 242 ARG cc_start: 0.8453 (tpt-90) cc_final: 0.8105 (tpp-160) REVERT: B 112 LYS cc_start: 0.7840 (ttmm) cc_final: 0.7382 (tptp) REVERT: B 240 LYS cc_start: 0.8386 (pttp) cc_final: 0.7996 (ptpt) REVERT: B 282 MET cc_start: 0.7216 (mmt) cc_final: 0.6641 (mmt) REVERT: C 80 MET cc_start: 0.7755 (mmt) cc_final: 0.7453 (mmt) REVERT: C 84 LEU cc_start: 0.8793 (mm) cc_final: 0.8423 (mm) REVERT: C 112 LYS cc_start: 0.7521 (mtmt) cc_final: 0.7282 (mttm) REVERT: C 203 MET cc_start: 0.8571 (mtm) cc_final: 0.8336 (mtm) REVERT: C 228 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.6301 (m-10) REVERT: C 322 GLU cc_start: 0.8345 (tp30) cc_final: 0.8039 (tp30) outliers start: 13 outliers final: 7 residues processed: 175 average time/residue: 0.0864 time to fit residues: 21.4087 Evaluate side-chains 170 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 227 LEU 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 342 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 45 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 32 optimal weight: 40.0000 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.216646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137326 restraints weight = 9566.951| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.15 r_work: 0.3415 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3212 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= 0.118 Angle : 0.537 17.600 13699 Z= 0.261 Chirality : 0.035 0.174 1616 Planarity : 0.004 0.048 1392 Dihedral : 19.742 173.813 2235 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.00 % Allowed : 13.43 % Favored : 84.57 % 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: 2.60 (0.28), residues: 975 helix: 2.38 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.87 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.009 0.001 TYR A 100 PHE 0.028 0.001 PHE A 107 TRP 0.024 0.001 TRP C 59 HIS 0.002 0.001 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9821) covalent geometry : angle 0.53726 / 0.26 (13699) hydrogen bonds : bond 0.03931 / 2.68 ( 626) hydrogen bonds : angle 3.52049 / 2.49 ( 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 181 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8149 (mtt) cc_final: 0.7620 (mtt) REVERT: B 112 LYS cc_start: 0.7840 (ttmm) cc_final: 0.7371 (tptp) REVERT: B 240 LYS cc_start: 0.8294 (pttp) cc_final: 0.7943 (ptpt) REVERT: B 282 MET cc_start: 0.7302 (mmt) cc_final: 0.6750 (mmt) REVERT: B 287 ARG cc_start: 0.7745 (mmm-85) cc_final: 0.7349 (mtt-85) REVERT: C 80 MET cc_start: 0.7787 (mmt) cc_final: 0.7490 (mmt) REVERT: C 84 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8452 (mm) REVERT: C 112 LYS cc_start: 0.7505 (mtmt) cc_final: 0.7206 (mttm) REVERT: C 134 MET cc_start: 0.8966 (ttm) cc_final: 0.8675 (mtt) REVERT: C 203 MET cc_start: 0.8566 (mtm) cc_final: 0.8341 (mtm) REVERT: C 228 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6245 (m-10) outliers start: 17 outliers final: 8 residues processed: 171 average time/residue: 0.0768 time to fit residues: 18.4428 Evaluate side-chains 167 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET 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 223 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 342 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 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 = 0.4461 r_free = 0.4461 target = 0.215715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.137454 restraints weight = 9499.867| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.17 r_work: 0.3399 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3337 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= 0.130 Angle : 0.554 17.601 13699 Z= 0.269 Chirality : 0.035 0.254 1616 Planarity : 0.004 0.047 1392 Dihedral : 19.715 173.902 2235 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.41 % Allowed : 14.25 % Favored : 84.33 % 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: 2.57 (0.27), residues: 975 helix: 2.34 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.82 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 297 TYR 0.010 0.001 TYR A 319 PHE 0.024 0.001 PHE A 107 TRP 0.021 0.001 TRP C 59 HIS 0.002 0.001 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9821) covalent geometry : angle 0.55376 / 0.27 (13699) hydrogen bonds : bond 0.04012 / 2.73 ( 626) hydrogen bonds : angle 3.52118 / 2.49 ( 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 174 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8195 (mtt) cc_final: 0.7716 (mtt) REVERT: A 287 ARG cc_start: 0.7433 (mtp180) cc_final: 0.7205 (mtp180) REVERT: B 240 LYS cc_start: 0.8374 (pttp) cc_final: 0.8006 (ptpt) REVERT: B 282 MET cc_start: 0.7335 (mmt) cc_final: 0.6786 (mmt) REVERT: B 287 ARG cc_start: 0.7807 (mmm-85) cc_final: 0.7416 (mtt-85) REVERT: C 80 MET cc_start: 0.7790 (mmt) cc_final: 0.7501 (mmt) REVERT: C 84 LEU cc_start: 0.8872 (mm) cc_final: 0.8515 (mm) REVERT: C 112 LYS cc_start: 0.7615 (mtmt) cc_final: 0.7370 (mttm) REVERT: C 203 MET cc_start: 0.8617 (mtm) cc_final: 0.8375 (mtm) REVERT: C 228 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6255 (m-10) REVERT: C 346 MET cc_start: 0.7825 (mmm) cc_final: 0.7419 (mmp) outliers start: 12 outliers final: 7 residues processed: 168 average time/residue: 0.0793 time to fit residues: 18.6548 Evaluate side-chains 167 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET 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 223 ILE Chi-restraints excluded: chain B residue 265 THR 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: 2.9990 chunk 54 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN ** 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 = 0.4458 r_free = 0.4458 target = 0.215587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137279 restraints weight = 9553.200| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.15 r_work: 0.3396 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3466 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= 0.129 Angle : 0.559 17.883 13699 Z= 0.268 Chirality : 0.036 0.364 1616 Planarity : 0.004 0.047 1392 Dihedral : 19.689 173.994 2235 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.30 % Allowed : 14.25 % Favored : 84.45 % 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: 2.80 (0.28), residues: 975 helix: 2.48 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.44 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 297 TYR 0.010 0.001 TYR A 319 PHE 0.025 0.001 PHE A 107 TRP 0.022 0.001 TRP C 59 HIS 0.001 0.001 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9821) covalent geometry : angle 0.55937 / 0.27 (13699) hydrogen bonds : bond 0.03989 / 2.71 ( 626) hydrogen bonds : angle 3.54173 / 2.51 ( 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 171 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8166 (mtt) cc_final: 0.7682 (mtt) REVERT: A 287 ARG cc_start: 0.7397 (mtp180) cc_final: 0.7168 (mtp180) REVERT: B 240 LYS cc_start: 0.8369 (pttp) cc_final: 0.7994 (ptpt) REVERT: B 282 MET cc_start: 0.7321 (mmt) cc_final: 0.6766 (mmt) REVERT: B 287 ARG cc_start: 0.7789 (mmm-85) cc_final: 0.7559 (mmm160) REVERT: C 80 MET cc_start: 0.7781 (mmt) cc_final: 0.7433 (mmt) REVERT: C 84 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8514 (mm) REVERT: C 112 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7353 (mttm) REVERT: C 134 MET cc_start: 0.8934 (ttm) cc_final: 0.8609 (mtt) REVERT: C 203 MET cc_start: 0.8625 (mtm) cc_final: 0.8378 (mtm) REVERT: C 227 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6310 (mp) REVERT: C 228 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6229 (m-10) REVERT: C 346 MET cc_start: 0.7820 (mmm) cc_final: 0.7391 (mmp) outliers start: 11 outliers final: 7 residues processed: 166 average time/residue: 0.0934 time to fit residues: 21.7521 Evaluate side-chains 166 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET 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 223 ILE Chi-restraints excluded: chain B residue 227 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: 4.9990 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 50.0000 chunk 87 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4431 r_free = 0.4431 target = 0.212377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.135444 restraints weight = 9549.797| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.07 r_work: 0.3365 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9821 Z= 0.177 Angle : 0.607 18.213 13699 Z= 0.293 Chirality : 0.039 0.331 1616 Planarity : 0.005 0.048 1392 Dihedral : 19.700 173.891 2235 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.18 % Allowed : 14.96 % Favored : 83.86 % 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: 2.33 (0.27), residues: 975 helix: 2.15 (0.19), residues: 753 sheet: None (None), residues: 0 loop : -0.57 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 287 TYR 0.016 0.002 TYR B 167 PHE 0.028 0.002 PHE C 307 TRP 0.024 0.002 TRP C 59 HIS 0.003 0.001 HIS B 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 9821) covalent geometry : angle 0.60741 / 0.29 (13699) hydrogen bonds : bond 0.04472 / 3.04 ( 626) hydrogen bonds : angle 3.65789 / 2.60 ( 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 170 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.8157 (mtt) cc_final: 0.7714 (mtt) REVERT: A 287 ARG cc_start: 0.7400 (mtp180) cc_final: 0.7160 (mtp180) REVERT: B 240 LYS cc_start: 0.8421 (pttp) cc_final: 0.7942 (ptpt) REVERT: B 282 MET cc_start: 0.7342 (mmt) cc_final: 0.6782 (mmt) REVERT: B 287 ARG cc_start: 0.7817 (mmm-85) cc_final: 0.7612 (mmm160) REVERT: C 73 MET cc_start: 0.4314 (tpt) cc_final: 0.3938 (tmm) REVERT: C 80 MET cc_start: 0.7801 (mmt) cc_final: 0.7436 (mmt) REVERT: C 84 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8550 (mm) REVERT: C 112 LYS cc_start: 0.7595 (mtmt) cc_final: 0.7383 (mttm) REVERT: C 134 MET cc_start: 0.9014 (ttm) cc_final: 0.8679 (mtt) REVERT: C 203 MET cc_start: 0.8665 (mtm) cc_final: 0.8421 (mtm) REVERT: C 227 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6291 (mp) REVERT: C 228 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6249 (m-10) REVERT: C 346 MET cc_start: 0.7779 (mmm) cc_final: 0.7385 (mmp) outliers start: 10 outliers final: 5 residues processed: 165 average time/residue: 0.1038 time to fit residues: 23.7744 Evaluate side-chains 165 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 CYS Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 227 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: 0.0970 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 40.0000 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 33 optimal weight: 40.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4451 r_free = 0.4451 target = 0.214616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.136226 restraints weight = 9442.197| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.12 r_work: 0.3390 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3743 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= 0.121 Angle : 0.579 18.314 13699 Z= 0.273 Chirality : 0.036 0.353 1616 Planarity : 0.005 0.046 1392 Dihedral : 19.663 173.960 2235 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.94 % Allowed : 15.19 % Favored : 83.86 % 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: 2.75 (0.28), residues: 975 helix: 2.45 (0.19), residues: 756 sheet: None (None), residues: 0 loop : -0.46 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 297 TYR 0.016 0.001 TYR A 100 PHE 0.026 0.001 PHE A 107 TRP 0.020 0.001 TRP C 59 HIS 0.003 0.000 HIS A 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 9821) covalent geometry : angle 0.57901 / 0.27 (13699) hydrogen bonds : bond 0.04006 / 2.73 ( 626) hydrogen bonds : angle 3.55421 / 2.51 ( 1744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2875.53 seconds wall clock time: 49 minutes 51.01 seconds (2991.01 seconds total)