Starting phenix.real_space_refine on Thu Jul 2 19:44:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjl_39344/07_2026/8yjl_39344.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjl_39344/07_2026/8yjl_39344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yjl_39344/07_2026/8yjl_39344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjl_39344/07_2026/8yjl_39344.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjl_39344/07_2026/8yjl_39344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjl_39344/07_2026/8yjl_39344.cif" } resolution = 3.51 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 253 atoms to isotropic. 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 58 5.49 5 S 63 5.16 5 C 6023 2.51 5 N 1652 2.21 5 O 2057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 9853 Number of models: 1 Model: "" Number of chains: 8 Chain: "J" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 344 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "F" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "C" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1968 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 248} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "D" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2770 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Time building chain proxies: 1.85, per 1000 atoms: 0.19 Number of scatterers: 9853 At special positions: 0 Unit cell: (102.92, 98.77, 103.75, 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 63 16.00 P 58 15.00 O 2057 8.00 N 1652 7.00 C 6023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 291.4 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 28.4% alpha, 27.2% beta 14 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 141 through 155 removed outlier: 4.014A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'B' and resid 8 through 19 removed outlier: 4.173A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 35 through 43 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 90 through 112 removed outlier: 3.860A pdb=" N GLY D 95 " --> pdb=" O GLN D 91 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 134 through 149 Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 180 through 186 removed outlier: 3.751A pdb=" N THR D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'D' and resid 219 through 230 Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.698A pdb=" N LEU D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 318 through 333 Processing helix chain 'D' and resid 339 through 344 removed outlier: 4.036A pdb=" N PHE D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 59 through 62 removed outlier: 4.397A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.591A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 34 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 122 through 125 removed outlier: 3.792A pdb=" N GLY D 348 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 203 through 208 removed outlier: 5.344A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.644A pdb=" N THR D 336 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.909A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER A 172 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA A 157 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS A 162 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A 203 " --> pdb=" O CYS A 162 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 71 removed outlier: 7.228A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 66 through 71 removed outlier: 7.129A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP A 29 " --> pdb=" O ASN A 36 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 18 through 21 Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.574A pdb=" N ALA D 174 " --> pdb=" O LYS D 30 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2396 1.33 - 1.45: 2045 1.45 - 1.57: 5464 1.57 - 1.70: 113 1.70 - 1.82: 102 Bond restraints: 10120 Sorted by residual: bond pdb=" C3' DA J 12 " pdb=" C2' DA J 12 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DA J 12 " pdb=" O3' DA J 12 " ideal model delta sigma weight residual 1.435 1.477 -0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" C3' DA F 9 " pdb=" C2' DA F 9 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.97e+00 bond pdb=" C1' DT J 13 " pdb=" N1 DT J 13 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.55e+00 bond pdb=" C3' DT F 8 " pdb=" C2' DT F 8 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.95e+00 ... (remaining 10115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 13603 3.03 - 6.06: 246 6.06 - 9.10: 44 9.10 - 12.13: 8 12.13 - 15.16: 2 Bond angle restraints: 13903 Sorted by residual: angle pdb=" CB MET B 199 " pdb=" CG MET B 199 " pdb=" SD MET B 199 " ideal model delta sigma weight residual 112.70 127.86 -15.16 3.00e+00 1.11e-01 2.55e+01 angle pdb=" C ASN B 187 " pdb=" N VAL B 188 " pdb=" CA VAL B 188 " ideal model delta sigma weight residual 121.97 131.00 -9.03 1.80e+00 3.09e-01 2.51e+01 angle pdb=" C ALA B 242 " pdb=" N ASP B 243 " pdb=" CA ASP B 243 " ideal model delta sigma weight residual 122.08 129.01 -6.93 1.47e+00 4.63e-01 2.22e+01 angle pdb=" N THR C 219 " pdb=" CA THR C 219 " pdb=" C THR C 219 " ideal model delta sigma weight residual 109.81 119.73 -9.92 2.21e+00 2.05e-01 2.02e+01 angle pdb=" CA ASP B 243 " pdb=" CB ASP B 243 " pdb=" CG ASP B 243 " ideal model delta sigma weight residual 112.60 116.91 -4.31 1.00e+00 1.00e+00 1.85e+01 ... (remaining 13898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.05: 5553 28.05 - 56.10: 522 56.10 - 84.16: 46 84.16 - 112.21: 6 112.21 - 140.26: 1 Dihedral angle restraints: 6128 sinusoidal: 2880 harmonic: 3248 Sorted by residual: dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 162 " pdb=" CB CYS A 162 " ideal model delta sinusoidal sigma weight residual -86.00 -173.26 87.26 1 1.00e+01 1.00e-02 9.14e+01 dihedral pdb=" CA GLU B 198 " pdb=" C GLU B 198 " pdb=" N MET B 199 " pdb=" CA MET B 199 " ideal model delta harmonic sigma weight residual -180.00 -153.73 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA GLU A 198 " pdb=" C GLU A 198 " pdb=" N MET A 199 " pdb=" CA MET A 199 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 6125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1303 0.073 - 0.146: 257 0.146 - 0.219: 33 0.219 - 0.292: 7 0.292 - 0.365: 1 Chirality restraints: 1601 Sorted by residual: chirality pdb=" CB VAL B 203 " pdb=" CA VAL B 203 " pdb=" CG1 VAL B 203 " pdb=" CG2 VAL B 203 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA THR C 219 " pdb=" N THR C 219 " pdb=" C THR C 219 " pdb=" CB THR C 219 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE A 11 " pdb=" CA ILE A 11 " pdb=" CG1 ILE A 11 " pdb=" CG2 ILE A 11 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1598 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 219 " 0.055 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO B 220 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 220 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 220 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " 0.046 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO A 220 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 109 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C LYS D 109 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS D 109 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN D 110 " -0.015 2.00e-02 2.50e+03 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3004 2.85 - 3.36: 8360 3.36 - 3.88: 17114 3.88 - 4.39: 19512 4.39 - 4.90: 32634 Nonbonded interactions: 80624 Sorted by model distance: nonbonded pdb=" O MET D 67 " pdb=" OG1 THR D 71 " model vdw 2.339 3.040 nonbonded pdb=" O GLU B 191 " pdb=" OG1 THR B 224 " model vdw 2.354 3.040 nonbonded pdb=" O ALA D 98 " pdb=" OG SER D 101 " model vdw 2.362 3.040 nonbonded pdb=" O VAL D 123 " pdb=" OG1 THR D 127 " model vdw 2.363 3.040 nonbonded pdb=" OE1 GLU D 221 " pdb=" NE2 HIS D 280 " model vdw 2.372 3.120 ... (remaining 80619 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' and (resid 1 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB )) or resid 110 through 254)) selection = (chain 'B' and (resid 1 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB )) or resid 110 through 254)) selection = (chain 'C' and resid 1 through 254) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.990 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10123 Z= 0.345 Angle : 1.035 15.161 13909 Z= 0.628 Chirality : 0.060 0.365 1601 Planarity : 0.007 0.081 1589 Dihedral : 19.381 140.260 4011 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -2.81 (0.21), residues: 1107 helix: -2.30 (0.22), residues: 315 sheet: -0.90 (0.26), residues: 357 loop : -2.18 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 261 TYR 0.024 0.003 TYR C 133 PHE 0.021 0.003 PHE D 283 TRP 0.015 0.002 TRP B 28 HIS 0.003 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.34 (10120) covalent geometry : angle 1.03489 / 0.63 (13903) SS BOND : bond 0.00130 / 0.08 ( 3) SS BOND : angle 0.97859 / 1.10 ( 6) hydrogen bonds : bond 0.13451 / 13.78 ( 489) hydrogen bonds : angle 7.71590 / 9.71 ( 1349) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.262 Fit side-chains REVERT: A 199 MET cc_start: 0.5430 (tpt) cc_final: 0.5024 (tpp) REVERT: A 244 MET cc_start: 0.7863 (tmm) cc_final: 0.7252 (ttt) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.0823 time to fit residues: 18.0088 Evaluate side-chains 111 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.0030 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 49 GLN A 49 GLN D 137 HIS D 253 HIS ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.156227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.121031 restraints weight = 12537.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124754 restraints weight = 10031.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126576 restraints weight = 6359.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.127050 restraints weight = 5314.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127472 restraints weight = 5163.361| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10123 Z= 0.161 Angle : 0.640 8.787 13909 Z= 0.346 Chirality : 0.047 0.257 1601 Planarity : 0.004 0.046 1589 Dihedral : 20.440 151.715 1871 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.93 % Allowed : 8.06 % Favored : 91.01 % 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: -2.09 (0.23), residues: 1107 helix: -0.94 (0.26), residues: 321 sheet: -0.99 (0.26), residues: 356 loop : -1.91 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 320 TYR 0.013 0.001 TYR B 211 PHE 0.013 0.001 PHE D 126 TRP 0.005 0.001 TRP D 274 HIS 0.016 0.002 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (10120) covalent geometry : angle 0.63985 / 0.35 (13903) SS BOND : bond 0.01319 / 1.32 ( 3) SS BOND : angle 1.05258 / 1.67 ( 6) hydrogen bonds : bond 0.04785 / 5.21 ( 489) hydrogen bonds : angle 6.18852 / 7.84 ( 1349) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.356 Fit side-chains REVERT: C 199 MET cc_start: 0.6129 (tpp) cc_final: 0.5814 (tpp) REVERT: A 244 MET cc_start: 0.8130 (tmm) cc_final: 0.7432 (ttt) outliers start: 9 outliers final: 8 residues processed: 130 average time/residue: 0.0886 time to fit residues: 16.9235 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 0.1980 chunk 78 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 137 HIS D 143 HIS D 302 ASN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.154252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118481 restraints weight = 12515.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121627 restraints weight = 10354.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123358 restraints weight = 6842.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124336 restraints weight = 5669.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124679 restraints weight = 5433.108| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10123 Z= 0.158 Angle : 0.605 9.589 13909 Z= 0.325 Chirality : 0.045 0.190 1601 Planarity : 0.004 0.042 1589 Dihedral : 20.596 152.489 1871 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.76 % Allowed : 11.05 % Favored : 87.19 % 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: -1.73 (0.23), residues: 1107 helix: -0.22 (0.28), residues: 317 sheet: -1.07 (0.26), residues: 356 loop : -1.78 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.013 0.001 TYR B 211 PHE 0.012 0.001 PHE D 126 TRP 0.003 0.001 TRP D 274 HIS 0.003 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (10120) covalent geometry : angle 0.60496 / 0.33 (13903) SS BOND : bond 0.00424 / 0.41 ( 3) SS BOND : angle 0.93066 / 1.13 ( 6) hydrogen bonds : bond 0.04119 / 4.32 ( 489) hydrogen bonds : angle 5.85818 / 7.49 ( 1349) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.307 Fit side-chains REVERT: A 244 MET cc_start: 0.8280 (tmm) cc_final: 0.7566 (ttt) outliers start: 17 outliers final: 14 residues processed: 128 average time/residue: 0.0779 time to fit residues: 14.7017 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 0.0070 chunk 109 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN D 137 HIS D 315 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.154423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117671 restraints weight = 12621.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121520 restraints weight = 9793.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123550 restraints weight = 6121.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124065 restraints weight = 5028.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124459 restraints weight = 4904.626| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10123 Z= 0.147 Angle : 0.583 9.537 13909 Z= 0.314 Chirality : 0.045 0.198 1601 Planarity : 0.003 0.037 1589 Dihedral : 20.483 146.779 1871 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.07 % Allowed : 12.29 % Favored : 85.64 % 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: -1.44 (0.24), residues: 1107 helix: 0.20 (0.29), residues: 317 sheet: -1.07 (0.26), residues: 363 loop : -1.60 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 47 TYR 0.013 0.001 TYR B 211 PHE 0.012 0.001 PHE D 126 TRP 0.003 0.001 TRP D 274 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (10120) covalent geometry : angle 0.58221 / 0.31 (13903) SS BOND : bond 0.00136 / 0.07 ( 3) SS BOND : angle 1.11225 / 1.83 ( 6) hydrogen bonds : bond 0.03706 / 3.95 ( 489) hydrogen bonds : angle 5.68548 / 7.23 ( 1349) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.319 Fit side-chains REVERT: C 72 LEU cc_start: 0.8662 (mt) cc_final: 0.8457 (mt) REVERT: B 27 CYS cc_start: 0.7265 (t) cc_final: 0.7004 (p) REVERT: B 68 MET cc_start: 0.8003 (mmt) cc_final: 0.7084 (mmt) REVERT: A 17 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: A 199 MET cc_start: 0.5484 (tpt) cc_final: 0.5242 (tpp) REVERT: A 244 MET cc_start: 0.8244 (tmm) cc_final: 0.7584 (ttm) REVERT: D 37 MET cc_start: 0.8145 (ttm) cc_final: 0.7907 (ttm) outliers start: 20 outliers final: 14 residues processed: 140 average time/residue: 0.0736 time to fit residues: 15.2617 Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 0.0040 chunk 59 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.0270 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.4650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 ASN D 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.154320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118370 restraints weight = 12530.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.121985 restraints weight = 9094.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123536 restraints weight = 5904.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124520 restraints weight = 5001.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124797 restraints weight = 4739.144| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10123 Z= 0.132 Angle : 0.571 10.489 13909 Z= 0.307 Chirality : 0.044 0.191 1601 Planarity : 0.003 0.031 1589 Dihedral : 20.420 143.991 1871 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.89 % Allowed : 13.74 % Favored : 83.37 % 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: -1.27 (0.24), residues: 1107 helix: 0.41 (0.30), residues: 317 sheet: -1.02 (0.26), residues: 358 loop : -1.49 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 261 TYR 0.012 0.001 TYR B 114 PHE 0.011 0.001 PHE D 126 TRP 0.004 0.001 TRP D 274 HIS 0.003 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10120) covalent geometry : angle 0.57070 / 0.31 (13903) SS BOND : bond 0.00075 / 0.07 ( 3) SS BOND : angle 0.78228 / 1.24 ( 6) hydrogen bonds : bond 0.03528 / 3.72 ( 489) hydrogen bonds : angle 5.58510 / 7.11 ( 1349) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.370 Fit side-chains REVERT: B 27 CYS cc_start: 0.7312 (t) cc_final: 0.7060 (p) REVERT: B 68 MET cc_start: 0.7959 (mmt) cc_final: 0.7150 (mmt) REVERT: A 17 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: A 199 MET cc_start: 0.5457 (tpt) cc_final: 0.5230 (tpp) REVERT: A 244 MET cc_start: 0.8217 (tmm) cc_final: 0.7637 (ttm) REVERT: D 37 MET cc_start: 0.8156 (ttm) cc_final: 0.7923 (ttt) outliers start: 28 outliers final: 21 residues processed: 137 average time/residue: 0.0825 time to fit residues: 16.6690 Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 23 optimal weight: 0.0170 chunk 50 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.153391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118157 restraints weight = 12609.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122196 restraints weight = 9494.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124539 restraints weight = 5962.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124512 restraints weight = 4995.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124925 restraints weight = 4631.349| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10123 Z= 0.134 Angle : 0.565 8.895 13909 Z= 0.304 Chirality : 0.044 0.187 1601 Planarity : 0.003 0.030 1589 Dihedral : 20.394 142.294 1871 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.38 % Allowed : 15.70 % Favored : 81.92 % 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: -1.15 (0.24), residues: 1107 helix: 0.52 (0.30), residues: 317 sheet: -0.97 (0.26), residues: 363 loop : -1.42 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 261 TYR 0.012 0.001 TYR B 211 PHE 0.011 0.001 PHE D 126 TRP 0.003 0.001 TRP D 274 HIS 0.002 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (10120) covalent geometry : angle 0.56436 / 0.30 (13903) SS BOND : bond 0.00048 / 0.03 ( 3) SS BOND : angle 0.84514 / 1.37 ( 6) hydrogen bonds : bond 0.03479 / 3.67 ( 489) hydrogen bonds : angle 5.53221 / 7.03 ( 1349) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.353 Fit side-chains REVERT: C 135 CYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7408 (t) REVERT: C 199 MET cc_start: 0.6437 (tpp) cc_final: 0.6222 (tpp) REVERT: B 27 CYS cc_start: 0.7308 (t) cc_final: 0.7069 (p) REVERT: B 68 MET cc_start: 0.7949 (mmt) cc_final: 0.7127 (mmt) REVERT: B 224 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8673 (p) REVERT: A 17 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: A 199 MET cc_start: 0.5453 (tpt) cc_final: 0.5223 (tpp) REVERT: A 244 MET cc_start: 0.8206 (tmm) cc_final: 0.7662 (ttm) REVERT: D 37 MET cc_start: 0.8202 (ttm) cc_final: 0.7963 (ttt) REVERT: D 143 HIS cc_start: 0.7010 (t70) cc_final: 0.6809 (t70) outliers start: 23 outliers final: 18 residues processed: 140 average time/residue: 0.0835 time to fit residues: 17.3477 Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 GLN ** D 112 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 = 0.3865 r_free = 0.3865 target = 0.151332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.115356 restraints weight = 12565.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118736 restraints weight = 9173.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120094 restraints weight = 5942.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120382 restraints weight = 5595.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124120 restraints weight = 4930.735| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10123 Z= 0.185 Angle : 0.606 9.165 13909 Z= 0.321 Chirality : 0.046 0.351 1601 Planarity : 0.003 0.030 1589 Dihedral : 20.439 139.685 1871 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.79 % Allowed : 16.12 % Favored : 81.10 % 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: -1.14 (0.24), residues: 1107 helix: 0.57 (0.30), residues: 314 sheet: -0.98 (0.27), residues: 363 loop : -1.42 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 129 TYR 0.015 0.002 TYR B 211 PHE 0.011 0.001 PHE D 126 TRP 0.005 0.001 TRP D 274 HIS 0.002 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (10120) covalent geometry : angle 0.60545 / 0.32 (13903) SS BOND : bond 0.00174 / 0.10 ( 3) SS BOND : angle 0.96076 / 1.39 ( 6) hydrogen bonds : bond 0.03657 / 3.90 ( 489) hydrogen bonds : angle 5.60674 / 7.13 ( 1349) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: C 135 CYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7435 (t) REVERT: B 27 CYS cc_start: 0.7353 (t) cc_final: 0.7107 (p) REVERT: B 68 MET cc_start: 0.7937 (mmt) cc_final: 0.7136 (mmt) REVERT: B 86 ASP cc_start: 0.6793 (m-30) cc_final: 0.6529 (m-30) REVERT: A 17 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: A 199 MET cc_start: 0.5547 (tpt) cc_final: 0.5308 (tpp) REVERT: A 244 MET cc_start: 0.8184 (tmm) cc_final: 0.7712 (ttm) REVERT: D 27 PHE cc_start: 0.6548 (t80) cc_final: 0.6326 (t80) REVERT: D 37 MET cc_start: 0.8249 (ttm) cc_final: 0.8027 (ttt) outliers start: 27 outliers final: 21 residues processed: 139 average time/residue: 0.0687 time to fit residues: 14.0501 Evaluate side-chains 138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 56 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 125 GLN ** D 112 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 = 0.3838 r_free = 0.3838 target = 0.148754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114853 restraints weight = 12770.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118062 restraints weight = 9157.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119463 restraints weight = 5931.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119851 restraints weight = 5496.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120582 restraints weight = 4906.406| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10123 Z= 0.155 Angle : 0.602 12.308 13909 Z= 0.315 Chirality : 0.045 0.185 1601 Planarity : 0.003 0.030 1589 Dihedral : 20.445 139.052 1871 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.89 % Allowed : 16.53 % Favored : 80.58 % 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: -1.08 (0.25), residues: 1107 helix: 0.62 (0.30), residues: 315 sheet: -0.96 (0.27), residues: 362 loop : -1.39 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.013 0.002 TYR B 211 PHE 0.010 0.001 PHE D 126 TRP 0.005 0.001 TRP D 274 HIS 0.002 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (10120) covalent geometry : angle 0.60148 / 0.32 (13903) SS BOND : bond 0.00106 / 0.05 ( 3) SS BOND : angle 0.96515 / 1.52 ( 6) hydrogen bonds : bond 0.03481 / 3.68 ( 489) hydrogen bonds : angle 5.58300 / 7.06 ( 1349) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: B 27 CYS cc_start: 0.7286 (t) cc_final: 0.7065 (p) REVERT: B 86 ASP cc_start: 0.6811 (m-30) cc_final: 0.6607 (m-30) REVERT: A 8 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7680 (pp30) REVERT: A 17 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: A 199 MET cc_start: 0.5543 (tpt) cc_final: 0.5328 (tpp) REVERT: A 244 MET cc_start: 0.8164 (tmm) cc_final: 0.7699 (ttm) REVERT: D 143 HIS cc_start: 0.7003 (t70) cc_final: 0.6736 (t70) outliers start: 28 outliers final: 21 residues processed: 141 average time/residue: 0.0698 time to fit residues: 14.5759 Evaluate side-chains 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 82 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN ** D 112 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 = 0.3845 r_free = 0.3845 target = 0.149417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115720 restraints weight = 12680.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118975 restraints weight = 9008.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120405 restraints weight = 5858.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120771 restraints weight = 5298.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.121274 restraints weight = 4809.486| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10123 Z= 0.133 Angle : 0.587 11.552 13909 Z= 0.308 Chirality : 0.044 0.259 1601 Planarity : 0.003 0.032 1589 Dihedral : 20.424 138.547 1871 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.38 % Allowed : 16.94 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.25), residues: 1107 helix: 0.70 (0.30), residues: 312 sheet: -0.86 (0.26), residues: 378 loop : -1.28 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 261 TYR 0.013 0.001 TYR B 211 PHE 0.012 0.001 PHE C 207 TRP 0.005 0.001 TRP D 274 HIS 0.002 0.000 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10120) covalent geometry : angle 0.58722 / 0.31 (13903) SS BOND : bond 0.00079 / 0.04 ( 3) SS BOND : angle 0.98132 / 1.51 ( 6) hydrogen bonds : bond 0.03378 / 3.56 ( 489) hydrogen bonds : angle 5.49757 / 6.95 ( 1349) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: C 135 CYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7413 (t) REVERT: B 27 CYS cc_start: 0.7301 (t) cc_final: 0.7100 (p) REVERT: B 86 ASP cc_start: 0.6795 (m-30) cc_final: 0.6588 (m-30) REVERT: A 8 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7681 (pp30) REVERT: A 17 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: A 199 MET cc_start: 0.5506 (tpt) cc_final: 0.5298 (tpp) REVERT: A 244 MET cc_start: 0.8173 (tmm) cc_final: 0.7712 (ttm) REVERT: D 143 HIS cc_start: 0.6983 (t70) cc_final: 0.6666 (t70) outliers start: 23 outliers final: 19 residues processed: 135 average time/residue: 0.0786 time to fit residues: 15.5629 Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 0 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN ** D 112 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 = 0.3831 r_free = 0.3831 target = 0.148198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114422 restraints weight = 12677.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.117448 restraints weight = 9018.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119171 restraints weight = 5964.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119429 restraints weight = 5438.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119986 restraints weight = 4804.094| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10123 Z= 0.180 Angle : 0.615 11.018 13909 Z= 0.320 Chirality : 0.046 0.297 1601 Planarity : 0.003 0.032 1589 Dihedral : 20.449 137.675 1871 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.38 % Allowed : 17.25 % Favored : 80.37 % 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: -1.00 (0.25), residues: 1107 helix: 0.68 (0.30), residues: 312 sheet: -0.94 (0.27), residues: 352 loop : -1.28 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.014 0.002 TYR B 211 PHE 0.010 0.001 PHE D 126 TRP 0.006 0.001 TRP D 274 HIS 0.002 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (10120) covalent geometry : angle 0.61432 / 0.32 (13903) SS BOND : bond 0.00138 / 0.08 ( 3) SS BOND : angle 1.00490 / 1.53 ( 6) hydrogen bonds : bond 0.03434 / 3.63 ( 489) hydrogen bonds : angle 5.53140 / 7.00 ( 1349) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: C 135 CYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7428 (t) REVERT: B 27 CYS cc_start: 0.7333 (t) cc_final: 0.7132 (p) REVERT: A 8 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7690 (pp30) REVERT: A 17 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: A 199 MET cc_start: 0.5555 (tpt) cc_final: 0.5342 (tpp) REVERT: A 244 MET cc_start: 0.8190 (tmm) cc_final: 0.7736 (ttm) REVERT: D 27 PHE cc_start: 0.6615 (t80) cc_final: 0.6401 (t80) REVERT: D 143 HIS cc_start: 0.7013 (t70) cc_final: 0.6703 (t70) outliers start: 23 outliers final: 20 residues processed: 134 average time/residue: 0.0679 time to fit residues: 13.4947 Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 112 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN ** D 112 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 = 0.3836 r_free = 0.3836 target = 0.148689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114861 restraints weight = 12720.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117899 restraints weight = 9014.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119588 restraints weight = 5965.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119859 restraints weight = 5483.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.120445 restraints weight = 4795.660| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10123 Z= 0.151 Angle : 0.611 10.946 13909 Z= 0.317 Chirality : 0.045 0.338 1601 Planarity : 0.003 0.032 1589 Dihedral : 20.460 137.318 1871 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.48 % Allowed : 16.94 % Favored : 80.58 % 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: -1.00 (0.25), residues: 1107 helix: 0.69 (0.30), residues: 312 sheet: -0.97 (0.27), residues: 352 loop : -1.26 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.013 0.002 TYR B 211 PHE 0.011 0.001 PHE D 316 TRP 0.006 0.001 TRP D 274 HIS 0.002 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (10120) covalent geometry : angle 0.61084 / 0.32 (13903) SS BOND : bond 0.00092 / 0.05 ( 3) SS BOND : angle 0.97550 / 1.52 ( 6) hydrogen bonds : bond 0.03382 / 3.59 ( 489) hydrogen bonds : angle 5.51889 / 6.98 ( 1349) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1366.62 seconds wall clock time: 24 minutes 27.99 seconds (1467.99 seconds total)