Starting phenix.real_space_refine on Wed Aug 5 13:04:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjl_39344/08_2026/8yjl_39344.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjl_39344/08_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_39344/08_2026/8yjl_39344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjl_39344/08_2026/8yjl_39344.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjl_39344/08_2026/8yjl_39344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjl_39344/08_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-2.2rc3-6140/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: 1.63, per 1000 atoms: 0.17 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: 0.64 Conformation dependent library (CDL) restraints added in 257.8 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: 1.10 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: 1.33 Time building geometry restraints manager: 0.86 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: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.260 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.060 ------------------------------------------------------------------------------- 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 : 1.036 15.161 13909 Z= 0.630 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 / 0.35 (10120) covalent geometry : angle 1.03586 / 0.63 (13903) SS BOND : bond 0.00130 / 0.08 ( 3) SS BOND : angle 0.97859 / 1.10 ( 6) hydrogen bonds : bond 0.13451 / 13.84 ( 489) hydrogen bonds : angle 7.71590 / 9.72 ( 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 : 0.221 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: 0.0714 time to fit residues: 15.7902 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 : 0.228 ------------------------------------------------------------------------------- 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 = 0.156299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121297 restraints weight = 12532.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125182 restraints weight = 9917.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127005 restraints weight = 6178.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127390 restraints weight = 5185.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127790 restraints weight = 5064.973| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10123 Z= 0.159 Angle : 0.637 8.394 13909 Z= 0.345 Chirality : 0.047 0.230 1601 Planarity : 0.004 0.048 1589 Dihedral : 20.363 149.608 1871 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: -2.12 (0.23), residues: 1107 helix: -1.00 (0.26), residues: 321 sheet: -0.98 (0.26), residues: 356 loop : -1.93 (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 0.012 0.001 PHE D 126 TRP 0.005 0.001 TRP B 28 HIS 0.007 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (10120) covalent geometry : angle 0.63629 / 0.34 (13903) SS BOND : bond 0.00502 / 0.50 ( 3) SS BOND : angle 1.01599 / 1.68 ( 6) hydrogen bonds : bond 0.04939 / 5.33 ( 489) hydrogen bonds : angle 6.23919 / 7.90 ( 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 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.362 Fit side-chains REVERT: C 199 MET cc_start: 0.6132 (tpp) cc_final: 0.5804 (tpp) REVERT: A 244 MET cc_start: 0.8120 (tmm) cc_final: 0.7403 (ttt) outliers start: 9 outliers final: 8 residues processed: 126 average time/residue: 0.0903 time to fit residues: 16.7320 Evaluate side-chains 120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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: 4.9990 chunk 93 optimal weight: 0.0070 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 137 HIS D 253 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 = 0.3900 r_free = 0.3900 target = 0.154199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119040 restraints weight = 12502.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122951 restraints weight = 9874.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124753 restraints weight = 6095.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125000 restraints weight = 5112.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125486 restraints weight = 4967.596| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1483 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= 0.162 Angle : 0.613 9.390 13909 Z= 0.328 Chirality : 0.046 0.207 1601 Planarity : 0.004 0.043 1589 Dihedral : 20.557 151.745 1871 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.24 % Allowed : 11.36 % Favored : 87.40 % 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: -1.77 (0.23), residues: 1107 helix: -0.26 (0.28), residues: 318 sheet: -1.08 (0.26), residues: 356 loop : -1.82 (0.25), residues: 433 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 0.013 0.001 PHE D 126 TRP 0.004 0.001 TRP D 274 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (10120) covalent geometry : angle 0.61310 / 0.33 (13903) SS BOND : bond 0.00451 / 0.44 ( 3) SS BOND : angle 0.94450 / 1.18 ( 6) hydrogen bonds : bond 0.04093 / 4.34 ( 489) hydrogen bonds : angle 5.89115 / 7.52 ( 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 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.384 Fit side-chains REVERT: A 244 MET cc_start: 0.8263 (tmm) cc_final: 0.7553 (ttt) outliers start: 12 outliers final: 8 residues processed: 125 average time/residue: 0.0886 time to fit residues: 16.3584 Evaluate side-chains 121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 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 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: 0.0670 chunk 109 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 44 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN D 137 HIS D 143 HIS D 315 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.155869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120039 restraints weight = 12613.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124388 restraints weight = 9476.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126340 restraints weight = 5695.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126584 restraints weight = 4680.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127107 restraints weight = 4576.071| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1734 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= 0.125 Angle : 0.568 9.751 13909 Z= 0.308 Chirality : 0.044 0.197 1601 Planarity : 0.003 0.039 1589 Dihedral : 20.466 147.405 1871 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.96 % Allowed : 12.09 % Favored : 85.95 % 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: 0.19 (0.29), residues: 317 sheet: -1.05 (0.26), residues: 363 loop : -1.60 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 47 TYR 0.011 0.001 TYR B 211 PHE 0.011 0.001 PHE D 126 TRP 0.003 0.001 TRP B 28 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (10120) covalent geometry : angle 0.56750 / 0.31 (13903) SS BOND : bond 0.00214 / 0.21 ( 3) SS BOND : angle 0.90757 / 1.28 ( 6) hydrogen bonds : bond 0.03685 / 3.91 ( 489) hydrogen bonds : angle 5.66587 / 7.21 ( 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 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.365 Fit side-chains REVERT: B 68 MET cc_start: 0.7988 (mmt) cc_final: 0.7168 (mmt) REVERT: A 17 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 244 MET cc_start: 0.8221 (tmm) cc_final: 0.7523 (ttm) REVERT: D 37 MET cc_start: 0.8118 (ttm) cc_final: 0.7872 (ttm) outliers start: 19 outliers final: 14 residues processed: 136 average time/residue: 0.0872 time to fit residues: 17.5064 Evaluate side-chains 127 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 ASP 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 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 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: 0.0570 chunk 59 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 73 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 48 GLN D 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.155714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119949 restraints weight = 12550.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124046 restraints weight = 9500.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125989 restraints weight = 5833.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126219 restraints weight = 4821.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126888 restraints weight = 4653.335| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10123 Z= 0.122 Angle : 0.566 10.137 13909 Z= 0.305 Chirality : 0.044 0.243 1601 Planarity : 0.003 0.036 1589 Dihedral : 20.381 144.176 1871 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.48 % Allowed : 13.64 % Favored : 83.88 % 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: -1.23 (0.24), residues: 1107 helix: 0.44 (0.30), residues: 316 sheet: -1.00 (0.26), residues: 363 loop : -1.47 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 261 TYR 0.011 0.001 TYR B 211 PHE 0.010 0.001 PHE D 126 TRP 0.004 0.001 TRP D 274 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (10120) covalent geometry : angle 0.56627 / 0.30 (13903) SS BOND : bond 0.00220 / 0.21 ( 3) SS BOND : angle 0.80586 / 1.19 ( 6) hydrogen bonds : bond 0.03534 / 3.73 ( 489) hydrogen bonds : angle 5.51829 / 7.00 ( 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 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.288 Fit side-chains REVERT: B 27 CYS cc_start: 0.7265 (t) cc_final: 0.7019 (p) REVERT: B 68 MET cc_start: 0.7959 (mmt) cc_final: 0.7131 (mmt) REVERT: A 17 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: A 199 MET cc_start: 0.5432 (tpt) cc_final: 0.5203 (tpp) REVERT: A 244 MET cc_start: 0.8239 (tmm) cc_final: 0.7573 (ttm) REVERT: D 37 MET cc_start: 0.8135 (ttm) cc_final: 0.7899 (ttm) outliers start: 24 outliers final: 17 residues processed: 134 average time/residue: 0.0875 time to fit residues: 17.1418 Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 96 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 ASN D 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.153603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.117763 restraints weight = 12639.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.121643 restraints weight = 9184.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123268 restraints weight = 5802.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124040 restraints weight = 4849.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124316 restraints weight = 4692.129| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10123 Z= 0.145 Angle : 0.569 8.719 13909 Z= 0.306 Chirality : 0.045 0.283 1601 Planarity : 0.003 0.030 1589 Dihedral : 20.376 141.903 1871 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.79 % Allowed : 14.46 % Favored : 82.75 % 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: -1.16 (0.24), residues: 1107 helix: 0.55 (0.30), residues: 316 sheet: -0.99 (0.26), residues: 363 loop : -1.44 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.012 0.001 TYR B 211 PHE 0.009 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 0.00312 / 0.14 (10120) covalent geometry : angle 0.56858 / 0.31 (13903) SS BOND : bond 0.00127 / 0.06 ( 3) SS BOND : angle 0.82145 / 1.16 ( 6) hydrogen bonds : bond 0.03515 / 3.72 ( 489) hydrogen bonds : angle 5.49338 / 6.96 ( 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 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: B 27 CYS cc_start: 0.7318 (t) cc_final: 0.7070 (p) REVERT: B 68 MET cc_start: 0.7960 (mmt) cc_final: 0.7125 (mmt) REVERT: A 17 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: A 199 MET cc_start: 0.5535 (tpt) cc_final: 0.5239 (tpp) REVERT: A 244 MET cc_start: 0.8214 (tmm) cc_final: 0.7648 (ttm) REVERT: D 37 MET cc_start: 0.8184 (ttm) cc_final: 0.7955 (ttt) outliers start: 27 outliers final: 19 residues processed: 140 average time/residue: 0.0845 time to fit residues: 17.6481 Evaluate side-chains 139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 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 A residue 216 THR 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: 0.7980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 125 GLN B 184 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.150772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114594 restraints weight = 12609.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116582 restraints weight = 11389.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118567 restraints weight = 7309.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119658 restraints weight = 5970.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120235 restraints weight = 5392.459| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10123 Z= 0.190 Angle : 0.606 8.778 13909 Z= 0.322 Chirality : 0.046 0.209 1601 Planarity : 0.003 0.030 1589 Dihedral : 20.436 139.324 1871 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.89 % Allowed : 15.81 % Favored : 81.30 % 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: -1.21 (0.24), residues: 1107 helix: 0.55 (0.30), residues: 314 sheet: -1.04 (0.26), residues: 363 loop : -1.47 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 261 TYR 0.014 0.002 TYR B 211 PHE 0.012 0.002 PHE B 2 TRP 0.006 0.001 TRP C 28 HIS 0.006 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (10120) covalent geometry : angle 0.60542 / 0.32 (13903) SS BOND : bond 0.00224 / 0.13 ( 3) SS BOND : angle 0.91037 / 1.22 ( 6) hydrogen bonds : bond 0.03635 / 3.90 ( 489) hydrogen bonds : angle 5.62181 / 7.19 ( 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 159 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: B 27 CYS cc_start: 0.7393 (t) cc_final: 0.7128 (p) REVERT: B 68 MET cc_start: 0.7949 (mmt) cc_final: 0.7171 (mmt) REVERT: B 86 ASP cc_start: 0.6899 (m-30) cc_final: 0.6658 (m-30) REVERT: A 17 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 146 ARG cc_start: 0.7641 (ttm110) cc_final: 0.7410 (ttm110) REVERT: A 199 MET cc_start: 0.5669 (tpt) cc_final: 0.5411 (tpp) REVERT: A 244 MET cc_start: 0.8212 (tmm) cc_final: 0.7747 (ttm) REVERT: D 27 PHE cc_start: 0.6571 (t80) cc_final: 0.6339 (t80) REVERT: D 37 MET cc_start: 0.8261 (ttm) cc_final: 0.8054 (ttt) outliers start: 28 outliers final: 21 residues processed: 147 average time/residue: 0.0861 time to fit residues: 18.4837 Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 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 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 A residue 216 THR 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: 0.5980 chunk 25 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN A 38 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.151414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115775 restraints weight = 12609.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117097 restraints weight = 7950.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120357 restraints weight = 6912.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120930 restraints weight = 5104.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122099 restraints weight = 4591.807| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2468 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= 0.156 Angle : 0.603 11.273 13909 Z= 0.318 Chirality : 0.046 0.209 1601 Planarity : 0.003 0.030 1589 Dihedral : 20.432 139.006 1871 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.20 % Allowed : 16.12 % 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: -1.16 (0.25), residues: 1107 helix: 0.63 (0.30), residues: 314 sheet: -1.05 (0.27), residues: 363 loop : -1.43 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.013 0.001 TYR B 211 PHE 0.011 0.001 PHE D 126 TRP 0.005 0.001 TRP D 274 HIS 0.006 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (10120) covalent geometry : angle 0.60288 / 0.32 (13903) SS BOND : bond 0.00131 / 0.08 ( 3) SS BOND : angle 1.07799 / 1.75 ( 6) hydrogen bonds : bond 0.03505 / 3.73 ( 489) hydrogen bonds : angle 5.60219 / 7.11 ( 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 155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: C 135 CYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7459 (t) REVERT: B 27 CYS cc_start: 0.7367 (t) cc_final: 0.7081 (p) REVERT: B 86 ASP cc_start: 0.6861 (m-30) cc_final: 0.6642 (m-30) REVERT: A 8 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7672 (pp30) REVERT: A 17 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: A 146 ARG cc_start: 0.7641 (ttm110) cc_final: 0.7405 (ttm110) REVERT: A 199 MET cc_start: 0.5616 (tpt) cc_final: 0.5379 (tpp) REVERT: A 244 MET cc_start: 0.8177 (tmm) cc_final: 0.7716 (ttm) REVERT: D 37 MET cc_start: 0.8229 (ttm) cc_final: 0.7996 (ttm) outliers start: 31 outliers final: 22 residues processed: 141 average time/residue: 0.0941 time to fit residues: 19.5002 Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 119 MET Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 139 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 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 A residue 216 THR 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: 0.7980 chunk 25 optimal weight: 0.0980 chunk 57 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 0.0570 chunk 86 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.149114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115395 restraints weight = 12715.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118571 restraints weight = 9003.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119888 restraints weight = 5869.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120092 restraints weight = 5487.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123277 restraints weight = 4874.194| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2499 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= 0.138 Angle : 0.598 10.863 13909 Z= 0.313 Chirality : 0.045 0.295 1601 Planarity : 0.003 0.030 1589 Dihedral : 20.419 138.741 1871 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.79 % Allowed : 16.32 % Favored : 80.89 % 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: -1.12 (0.25), residues: 1107 helix: 0.65 (0.30), residues: 315 sheet: -1.05 (0.26), residues: 358 loop : -1.37 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.013 0.001 TYR B 211 PHE 0.011 0.001 PHE D 126 TRP 0.005 0.001 TRP D 274 HIS 0.006 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (10120) covalent geometry : angle 0.59824 / 0.31 (13903) SS BOND : bond 0.00074 / 0.04 ( 3) SS BOND : angle 1.02659 / 1.65 ( 6) hydrogen bonds : bond 0.03438 / 3.65 ( 489) hydrogen bonds : angle 5.55859 / 7.04 ( 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 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: C 135 CYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7412 (t) REVERT: B 86 ASP cc_start: 0.6801 (m-30) cc_final: 0.6599 (m-30) REVERT: A 8 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7687 (pp30) REVERT: A 17 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 146 ARG cc_start: 0.7611 (ttm110) cc_final: 0.7385 (ttm110) REVERT: A 244 MET cc_start: 0.8149 (tmm) cc_final: 0.7696 (ttm) outliers start: 27 outliers final: 21 residues processed: 131 average time/residue: 0.0847 time to fit residues: 16.1936 Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 119 MET Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 139 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 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 A residue 216 THR 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: 0.8980 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 88 optimal weight: 0.0970 chunk 22 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN 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 = 0.148449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114847 restraints weight = 12683.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117894 restraints weight = 8965.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.119597 restraints weight = 5928.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119694 restraints weight = 5515.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120990 restraints weight = 4793.649| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10123 Z= 0.158 Angle : 0.615 11.277 13909 Z= 0.319 Chirality : 0.046 0.347 1601 Planarity : 0.003 0.032 1589 Dihedral : 20.427 138.092 1871 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.48 % Allowed : 16.84 % 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: -1.10 (0.24), residues: 1107 helix: 0.64 (0.30), residues: 315 sheet: -1.02 (0.27), residues: 348 loop : -1.36 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.013 0.001 TYR B 211 PHE 0.011 0.001 PHE D 126 TRP 0.006 0.001 TRP D 274 HIS 0.006 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (10120) covalent geometry : angle 0.61482 / 0.32 (13903) SS BOND : bond 0.00141 / 0.10 ( 3) SS BOND : angle 1.04452 / 1.64 ( 6) hydrogen bonds : bond 0.03441 / 3.65 ( 489) hydrogen bonds : angle 5.56334 / 7.04 ( 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 148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: B 86 ASP cc_start: 0.6849 (m-30) cc_final: 0.6633 (m-30) REVERT: A 8 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7682 (pp30) REVERT: A 17 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: A 146 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7409 (ttm110) REVERT: A 199 MET cc_start: 0.7222 (tpp) cc_final: 0.6501 (tpt) REVERT: A 244 MET cc_start: 0.8153 (tmm) cc_final: 0.7723 (ttm) REVERT: D 40 TYR cc_start: 0.8878 (m-80) cc_final: 0.8443 (m-10) outliers start: 24 outliers final: 20 residues processed: 136 average time/residue: 0.0901 time to fit residues: 17.8680 Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 119 MET Chi-restraints excluded: chain C residue 139 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 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 95 optimal weight: 0.0870 chunk 110 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN C 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114829 restraints weight = 12759.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.117882 restraints weight = 8966.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119113 restraints weight = 5938.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119258 restraints weight = 5694.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.121856 restraints weight = 4980.771| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.003 0.061 10123 Z= 0.157 Angle : 0.617 11.279 13909 Z= 0.320 Chirality : 0.046 0.424 1601 Planarity : 0.003 0.032 1589 Dihedral : 20.436 137.609 1871 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.58 % Allowed : 16.94 % Favored : 80.48 % 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: -1.05 (0.25), residues: 1107 helix: 0.69 (0.30), residues: 312 sheet: -1.03 (0.27), residues: 348 loop : -1.31 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 261 TYR 0.013 0.001 TYR B 211 PHE 0.011 0.001 PHE D 126 TRP 0.006 0.001 TRP D 274 HIS 0.006 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (10120) covalent geometry : angle 0.61716 / 0.32 (13903) SS BOND : bond 0.00114 / 0.08 ( 3) SS BOND : angle 1.00740 / 1.58 ( 6) hydrogen bonds : bond 0.03422 / 3.64 ( 489) hydrogen bonds : angle 5.55298 / 7.02 ( 1349) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1540.74 seconds wall clock time: 27 minutes 31.25 seconds (1651.25 seconds total)