Starting phenix.real_space_refine on Fri Aug 22 13:20:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pqq_13596/08_2025/7pqq_13596.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pqq_13596/08_2025/7pqq_13596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pqq_13596/08_2025/7pqq_13596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pqq_13596/08_2025/7pqq_13596.map" model { file = "/net/cci-nas-00/data/ceres_data/7pqq_13596/08_2025/7pqq_13596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pqq_13596/08_2025/7pqq_13596.cif" } resolution = 3.3 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 2105 2.51 5 N 516 2.21 5 O 555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3207 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2279 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 281} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 1 Time building chain proxies: 1.09, per 1000 atoms: 0.34 Number of scatterers: 3207 At special positions: 0 Unit cell: (56.448, 81.648, 96.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 555 8.00 N 516 7.00 C 2105 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 793 " - pdb=" SG CYS B 866 " 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: 0.28 Conformation dependent library (CDL) restraints added in 127.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 57.1% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 23 through 30 removed outlier: 3.955A pdb=" N SER A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.533A pdb=" N ILE A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 50 through 57 removed outlier: 3.542A pdb=" N LYS A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 removed outlier: 4.588A pdb=" N ILE A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 88 through 99 removed outlier: 3.788A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.506A pdb=" N SER A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 111' Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.519A pdb=" N SER A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 156 through 180 removed outlier: 3.551A pdb=" N VAL A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 4.240A pdb=" N ILE A 174 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LYS A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 210 removed outlier: 4.208A pdb=" N ARG A 185 " --> pdb=" O PRO A 181 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLY A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 4.081A pdb=" N ALA A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 218' Processing helix chain 'A' and resid 219 through 243 removed outlier: 3.527A pdb=" N ALA A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.777A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.693A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.737A pdb=" N ILE A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.505A pdb=" N ILE A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 307 removed outlier: 4.486A pdb=" N LEU A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 883 removed outlier: 3.941A pdb=" N LEU B 882 " --> pdb=" O SER B 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.777A pdb=" N LEU B 791 " --> pdb=" O LEU B 851 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 815 through 822 removed outlier: 6.773A pdb=" N TRP B 806 " --> pdb=" O VAL B 818 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE B 820 " --> pdb=" O MET B 804 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET B 804 " --> pdb=" O PHE B 820 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 803 " --> pdb=" O ALA B 869 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 815 through 822 removed outlier: 6.773A pdb=" N TRP B 806 " --> pdb=" O VAL B 818 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE B 820 " --> pdb=" O MET B 804 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET B 804 " --> pdb=" O PHE B 820 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 803 " --> pdb=" O ALA B 869 " (cutoff:3.500A) 140 hydrogen bonds defined for protein. 402 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.36 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 971 1.34 - 1.46: 755 1.46 - 1.58: 1499 1.58 - 1.70: 0 1.70 - 1.81: 49 Bond restraints: 3274 Sorted by residual: bond pdb=" C ARG A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.30e-02 5.92e+03 2.68e+00 bond pdb=" CB VAL B 834 " pdb=" CG2 VAL B 834 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 bond pdb=" CA PHE A 244 " pdb=" C PHE A 244 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.59e-02 3.96e+03 1.19e+00 bond pdb=" CB VAL B 894 " pdb=" CG2 VAL B 894 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.13e-01 bond pdb=" C PHE A 274 " pdb=" N PRO A 275 " ideal model delta sigma weight residual 1.329 1.339 -0.009 1.18e-02 7.18e+03 6.36e-01 ... (remaining 3269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 4285 1.59 - 3.18: 128 3.18 - 4.77: 16 4.77 - 6.36: 8 6.36 - 7.95: 2 Bond angle restraints: 4439 Sorted by residual: angle pdb=" N ILE A 161 " pdb=" CA ILE A 161 " pdb=" C ILE A 161 " ideal model delta sigma weight residual 113.00 109.11 3.89 1.30e+00 5.92e-01 8.97e+00 angle pdb=" CB MET A 72 " pdb=" CG MET A 72 " pdb=" SD MET A 72 " ideal model delta sigma weight residual 112.70 120.65 -7.95 3.00e+00 1.11e-01 7.03e+00 angle pdb=" NE ARG B 815 " pdb=" CZ ARG B 815 " pdb=" NH1 ARG B 815 " ideal model delta sigma weight residual 121.50 119.01 2.49 1.00e+00 1.00e+00 6.18e+00 angle pdb=" N PRO A 15 " pdb=" CA PRO A 15 " pdb=" C PRO A 15 " ideal model delta sigma weight residual 110.70 113.16 -2.46 1.22e+00 6.72e-01 4.08e+00 angle pdb=" CA LEU B 789 " pdb=" CB LEU B 789 " pdb=" CG LEU B 789 " ideal model delta sigma weight residual 116.30 123.19 -6.89 3.50e+00 8.16e-02 3.88e+00 ... (remaining 4434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 1705 15.89 - 31.78: 186 31.78 - 47.67: 50 47.67 - 63.56: 5 63.56 - 79.46: 2 Dihedral angle restraints: 1948 sinusoidal: 750 harmonic: 1198 Sorted by residual: dihedral pdb=" CA PHE A 274 " pdb=" C PHE A 274 " pdb=" N PRO A 275 " pdb=" CA PRO A 275 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PHE A 304 " pdb=" C PHE A 304 " pdb=" N TRP A 305 " pdb=" CA TRP A 305 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLU B 814 " pdb=" CB GLU B 814 " pdb=" CG GLU B 814 " pdb=" CD GLU B 814 " ideal model delta sinusoidal sigma weight residual -60.00 -114.43 54.43 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 1945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 284 0.028 - 0.057: 165 0.057 - 0.085: 55 0.085 - 0.113: 22 0.113 - 0.142: 4 Chirality restraints: 530 Sorted by residual: chirality pdb=" CB VAL B 834 " pdb=" CA VAL B 834 " pdb=" CG1 VAL B 834 " pdb=" CG2 VAL B 834 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA PRO B 858 " pdb=" N PRO B 858 " pdb=" C PRO B 858 " pdb=" CB PRO B 858 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL A 154 " pdb=" N VAL A 154 " pdb=" C VAL A 154 " pdb=" CB VAL A 154 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 527 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 825 " -0.010 2.00e-02 2.50e+03 1.23e-02 3.01e+00 pdb=" CG TYR B 825 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 825 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 825 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 825 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 825 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 825 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 825 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 838 " 0.001 2.00e-02 2.50e+03 1.05e-02 1.92e+00 pdb=" CG PHE B 838 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE B 838 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 838 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 838 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 838 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 838 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 244 " -0.008 2.00e-02 2.50e+03 9.87e-03 1.70e+00 pdb=" CG PHE A 244 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 244 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 244 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 244 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 244 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 244 " -0.001 2.00e-02 2.50e+03 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 710 2.78 - 3.31: 3155 3.31 - 3.84: 4893 3.84 - 4.37: 6108 4.37 - 4.90: 10318 Nonbonded interactions: 25184 Sorted by model distance: nonbonded pdb=" O ALA A 111 " pdb=" NE1 TRP A 305 " model vdw 2.244 3.120 nonbonded pdb=" O ASN A 17 " pdb=" NZ LYS A 20 " model vdw 2.290 3.120 nonbonded pdb=" N ASP A 115 " pdb=" OG1 THR A 253 " model vdw 2.431 3.120 nonbonded pdb=" N GLY A 19 " pdb=" OD2 ASP A 24 " model vdw 2.438 3.120 nonbonded pdb=" OG1 THR A 13 " pdb=" N LEU A 14 " model vdw 2.478 3.120 ... (remaining 25179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.030 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3275 Z= 0.176 Angle : 0.686 7.954 4441 Z= 0.368 Chirality : 0.041 0.142 530 Planarity : 0.004 0.032 540 Dihedral : 14.020 79.456 1179 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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 aren not related in a simple way. whole: -2.50 (0.40), residues: 411 helix: -1.59 (0.36), residues: 194 sheet: -1.56 (0.81), residues: 40 loop : -1.58 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 800 TYR 0.031 0.003 TYR B 825 PHE 0.023 0.002 PHE A 244 TRP 0.011 0.002 TRP B 823 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3274) covalent geometry : angle 0.68540 ( 4439) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.92220 ( 2) hydrogen bonds : bond 0.28113 ( 130) hydrogen bonds : angle 10.59423 ( 402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.100 Fit side-chains REVERT: A 72 MET cc_start: 0.7274 (mmm) cc_final: 0.7008 (mmp) REVERT: A 228 LEU cc_start: 0.8634 (tp) cc_final: 0.8225 (tt) REVERT: A 257 GLU cc_start: 0.7612 (tp30) cc_final: 0.7404 (tp30) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0553 time to fit residues: 7.0313 Evaluate side-chains 89 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 0.0270 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN B 824 ASN B 888 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.165117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.148253 restraints weight = 5107.797| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.77 r_work: 0.3817 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3275 Z= 0.130 Angle : 0.639 7.910 4441 Z= 0.313 Chirality : 0.041 0.139 530 Planarity : 0.005 0.036 540 Dihedral : 4.599 20.987 447 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.98 % Allowed : 14.16 % Favored : 83.85 % 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 aren not related in a simple way. whole: -2.25 (0.39), residues: 411 helix: -1.40 (0.34), residues: 201 sheet: -1.23 (0.80), residues: 40 loop : -1.47 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 252 TYR 0.018 0.002 TYR A 238 PHE 0.020 0.002 PHE A 128 TRP 0.010 0.001 TRP A 56 HIS 0.001 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3274) covalent geometry : angle 0.63858 ( 4439) SS BOND : bond 0.00050 ( 1) SS BOND : angle 0.48456 ( 2) hydrogen bonds : bond 0.04598 ( 130) hydrogen bonds : angle 5.72282 ( 402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.124 Fit side-chains REVERT: A 72 MET cc_start: 0.7955 (mmm) cc_final: 0.7516 (mmp) outliers start: 7 outliers final: 5 residues processed: 89 average time/residue: 0.0459 time to fit residues: 5.2696 Evaluate side-chains 90 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 847 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.163375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.146571 restraints weight = 5016.224| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.70 r_work: 0.3800 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3275 Z= 0.148 Angle : 0.620 9.134 4441 Z= 0.300 Chirality : 0.041 0.130 530 Planarity : 0.005 0.036 540 Dihedral : 4.431 19.930 447 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.12 % Allowed : 18.13 % Favored : 78.75 % 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 aren not related in a simple way. whole: -2.01 (0.40), residues: 411 helix: -1.14 (0.35), residues: 203 sheet: -1.11 (0.81), residues: 40 loop : -1.44 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 837 TYR 0.013 0.002 TYR A 186 PHE 0.015 0.002 PHE A 128 TRP 0.007 0.001 TRP A 56 HIS 0.001 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3274) covalent geometry : angle 0.61956 ( 4439) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.62080 ( 2) hydrogen bonds : bond 0.03941 ( 130) hydrogen bonds : angle 5.23362 ( 402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.140 Fit side-chains REVERT: A 30 ILE cc_start: 0.7623 (mt) cc_final: 0.7401 (tt) outliers start: 11 outliers final: 9 residues processed: 93 average time/residue: 0.0543 time to fit residues: 6.4976 Evaluate side-chains 91 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.164181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.147560 restraints weight = 4955.685| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.70 r_work: 0.3805 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3275 Z= 0.138 Angle : 0.618 8.527 4441 Z= 0.295 Chirality : 0.041 0.130 530 Planarity : 0.004 0.036 540 Dihedral : 4.291 18.943 447 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.10 % Allowed : 20.40 % Favored : 74.50 % 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 aren not related in a simple way. whole: -1.90 (0.40), residues: 411 helix: -1.04 (0.35), residues: 201 sheet: -1.00 (0.85), residues: 39 loop : -1.41 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 252 TYR 0.012 0.002 TYR B 883 PHE 0.013 0.001 PHE A 292 TRP 0.005 0.001 TRP A 56 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3274) covalent geometry : angle 0.61788 ( 4439) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.66871 ( 2) hydrogen bonds : bond 0.03316 ( 130) hydrogen bonds : angle 4.98639 ( 402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.127 Fit side-chains REVERT: A 72 MET cc_start: 0.7961 (mmm) cc_final: 0.7584 (mmp) REVERT: A 288 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8875 (tp) outliers start: 18 outliers final: 11 residues processed: 95 average time/residue: 0.0520 time to fit residues: 6.4035 Evaluate side-chains 94 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN B 824 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.163310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.146590 restraints weight = 5021.743| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.72 r_work: 0.3800 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3275 Z= 0.143 Angle : 0.627 10.029 4441 Z= 0.300 Chirality : 0.041 0.126 530 Planarity : 0.004 0.035 540 Dihedral : 4.261 18.032 447 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.25 % Allowed : 22.10 % Favored : 73.65 % 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 aren not related in a simple way. whole: -1.81 (0.40), residues: 411 helix: -0.93 (0.36), residues: 202 sheet: -1.24 (0.82), residues: 40 loop : -1.35 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 837 TYR 0.012 0.002 TYR B 883 PHE 0.012 0.001 PHE B 817 TRP 0.004 0.001 TRP A 56 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3274) covalent geometry : angle 0.62692 ( 4439) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.89280 ( 2) hydrogen bonds : bond 0.03164 ( 130) hydrogen bonds : angle 4.96958 ( 402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.137 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 0.0527 time to fit residues: 6.0811 Evaluate side-chains 88 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 15 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.163532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.146649 restraints weight = 4939.642| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.79 r_work: 0.3793 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3275 Z= 0.111 Angle : 0.613 8.847 4441 Z= 0.286 Chirality : 0.039 0.126 530 Planarity : 0.004 0.036 540 Dihedral : 4.041 16.808 447 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.25 % Allowed : 21.53 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.40), residues: 411 helix: -0.81 (0.35), residues: 200 sheet: -1.11 (0.82), residues: 40 loop : -1.49 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 837 TYR 0.010 0.001 TYR B 883 PHE 0.010 0.001 PHE A 292 TRP 0.004 0.001 TRP A 56 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3274) covalent geometry : angle 0.61281 ( 4439) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.62593 ( 2) hydrogen bonds : bond 0.02772 ( 130) hydrogen bonds : angle 4.75773 ( 402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.088 Fit side-chains REVERT: A 72 MET cc_start: 0.8035 (mmm) cc_final: 0.7681 (mmp) REVERT: A 257 GLU cc_start: 0.8222 (tp30) cc_final: 0.7859 (tp30) REVERT: A 264 GLN cc_start: 0.7995 (pm20) cc_final: 0.7757 (pm20) REVERT: A 285 PHE cc_start: 0.8624 (t80) cc_final: 0.8299 (t80) REVERT: B 816 GLU cc_start: 0.8079 (mp0) cc_final: 0.7764 (mp0) REVERT: B 859 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7557 (mt-10) outliers start: 15 outliers final: 12 residues processed: 93 average time/residue: 0.0569 time to fit residues: 6.6712 Evaluate side-chains 94 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.164965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.147537 restraints weight = 5102.632| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.00 r_work: 0.3795 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3275 Z= 0.103 Angle : 0.587 8.827 4441 Z= 0.275 Chirality : 0.039 0.121 530 Planarity : 0.004 0.037 540 Dihedral : 3.874 15.339 447 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.53 % Allowed : 20.68 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.41), residues: 411 helix: -0.55 (0.37), residues: 198 sheet: -1.06 (0.81), residues: 40 loop : -1.44 (0.47), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 800 TYR 0.010 0.001 TYR B 883 PHE 0.011 0.001 PHE A 292 TRP 0.004 0.001 TRP A 56 HIS 0.001 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 3274) covalent geometry : angle 0.58688 ( 4439) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.67682 ( 2) hydrogen bonds : bond 0.02617 ( 130) hydrogen bonds : angle 4.62881 ( 402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.077 Fit side-chains REVERT: A 146 TYR cc_start: 0.8849 (t80) cc_final: 0.8639 (t80) REVERT: A 257 GLU cc_start: 0.8248 (tp30) cc_final: 0.7892 (tp30) REVERT: A 285 PHE cc_start: 0.8618 (t80) cc_final: 0.8326 (t80) REVERT: B 859 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7622 (mt-10) outliers start: 16 outliers final: 15 residues processed: 87 average time/residue: 0.0532 time to fit residues: 5.8288 Evaluate side-chains 91 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.162966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145764 restraints weight = 5120.035| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.91 r_work: 0.3777 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3275 Z= 0.129 Angle : 0.617 8.455 4441 Z= 0.289 Chirality : 0.040 0.123 530 Planarity : 0.004 0.035 540 Dihedral : 3.929 14.715 447 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.40 % Allowed : 22.66 % Favored : 73.94 % 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 aren not related in a simple way. whole: -1.60 (0.40), residues: 411 helix: -0.58 (0.36), residues: 199 sheet: -1.10 (0.80), residues: 40 loop : -1.50 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 837 TYR 0.011 0.001 TYR B 883 PHE 0.018 0.001 PHE A 128 TRP 0.004 0.001 TRP A 305 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3274) covalent geometry : angle 0.61653 ( 4439) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.62853 ( 2) hydrogen bonds : bond 0.02696 ( 130) hydrogen bonds : angle 4.73211 ( 402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.127 Fit side-chains REVERT: A 72 MET cc_start: 0.8116 (mmm) cc_final: 0.7756 (mmp) REVERT: A 146 TYR cc_start: 0.8874 (t80) cc_final: 0.8672 (t80) REVERT: A 285 PHE cc_start: 0.8644 (t80) cc_final: 0.8295 (t80) REVERT: A 288 LEU cc_start: 0.9076 (tt) cc_final: 0.8858 (tp) outliers start: 12 outliers final: 12 residues processed: 88 average time/residue: 0.0564 time to fit residues: 6.2984 Evaluate side-chains 92 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.161782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144480 restraints weight = 5030.751| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.93 r_work: 0.3767 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3275 Z= 0.136 Angle : 0.628 7.985 4441 Z= 0.297 Chirality : 0.040 0.125 530 Planarity : 0.004 0.035 540 Dihedral : 3.967 14.497 447 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.40 % Allowed : 23.80 % Favored : 72.80 % 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 aren not related in a simple way. whole: -1.62 (0.40), residues: 411 helix: -0.59 (0.36), residues: 199 sheet: -1.13 (0.80), residues: 40 loop : -1.52 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 837 TYR 0.012 0.002 TYR A 69 PHE 0.010 0.001 PHE A 292 TRP 0.005 0.001 TRP A 305 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3274) covalent geometry : angle 0.62835 ( 4439) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.68023 ( 2) hydrogen bonds : bond 0.02749 ( 130) hydrogen bonds : angle 4.77435 ( 402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.127 Fit side-chains REVERT: A 72 MET cc_start: 0.8169 (mmm) cc_final: 0.7807 (mmp) REVERT: A 146 TYR cc_start: 0.8890 (t80) cc_final: 0.8683 (t80) REVERT: A 288 LEU cc_start: 0.9075 (tt) cc_final: 0.8849 (tp) REVERT: B 816 GLU cc_start: 0.8130 (mp0) cc_final: 0.7828 (mp0) outliers start: 12 outliers final: 12 residues processed: 89 average time/residue: 0.0537 time to fit residues: 6.0535 Evaluate side-chains 93 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.0370 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.162431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.145699 restraints weight = 4987.748| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.80 r_work: 0.3786 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3275 Z= 0.120 Angle : 0.617 8.210 4441 Z= 0.290 Chirality : 0.039 0.123 530 Planarity : 0.004 0.036 540 Dihedral : 3.916 14.008 447 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.97 % Allowed : 24.08 % Favored : 71.95 % 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 aren not related in a simple way. whole: -1.55 (0.40), residues: 411 helix: -0.55 (0.36), residues: 199 sheet: -1.06 (0.80), residues: 40 loop : -1.47 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 800 TYR 0.011 0.001 TYR B 883 PHE 0.018 0.001 PHE A 128 TRP 0.004 0.001 TRP A 56 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 3274) covalent geometry : angle 0.61719 ( 4439) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.64862 ( 2) hydrogen bonds : bond 0.02653 ( 130) hydrogen bonds : angle 4.74645 ( 402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.148 Fit side-chains REVERT: A 285 PHE cc_start: 0.8616 (t80) cc_final: 0.8297 (t80) REVERT: A 288 LEU cc_start: 0.9055 (tt) cc_final: 0.8846 (tp) REVERT: B 816 GLU cc_start: 0.8101 (mp0) cc_final: 0.7802 (mp0) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.0559 time to fit residues: 6.4230 Evaluate side-chains 92 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 793 CYS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 863 VAL Chi-restraints excluded: chain B residue 879 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.161729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.144470 restraints weight = 5084.969| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.87 r_work: 0.3770 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3275 Z= 0.136 Angle : 0.607 7.836 4441 Z= 0.292 Chirality : 0.040 0.122 530 Planarity : 0.004 0.035 540 Dihedral : 3.960 13.625 447 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.68 % Allowed : 24.36 % Favored : 71.95 % 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 aren not related in a simple way. whole: -1.55 (0.41), residues: 411 helix: -0.56 (0.36), residues: 200 sheet: -1.03 (0.80), residues: 40 loop : -1.46 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 837 TYR 0.011 0.002 TYR B 883 PHE 0.011 0.001 PHE A 292 TRP 0.005 0.001 TRP A 305 HIS 0.001 0.000 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3274) covalent geometry : angle 0.60692 ( 4439) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.64332 ( 2) hydrogen bonds : bond 0.02736 ( 130) hydrogen bonds : angle 4.74458 ( 402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1131.80 seconds wall clock time: 20 minutes 3.31 seconds (1203.31 seconds total)