Starting phenix.real_space_refine on Fri Sep 11 11:55:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d7l_7823/09_2026/6d7l_7823.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d7l_7823/09_2026/6d7l_7823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6d7l_7823/09_2026/6d7l_7823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d7l_7823/09_2026/6d7l_7823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6d7l_7823/09_2026/6d7l_7823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d7l_7823/09_2026/6d7l_7823.map" } resolution = 4.0 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= 0.005 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 56 5.16 5 C 5760 2.51 5 N 1584 2.21 5 O 1772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9172 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2293 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 2 Restraints were copied for chains: B, C, D Time building chain proxies: 1.95, per 1000 atoms: 0.21 Number of scatterers: 9172 At special positions: 0 Unit cell: (108.504, 108.504, 78.912, 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 56 16.00 O 1772 8.00 N 1584 7.00 C 5760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 324.2 milliseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 69.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 37 through 49 removed outlier: 3.847A pdb=" N TYR A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.859A pdb=" N VAL A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.604A pdb=" N ALA A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.828A pdb=" N HIS A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.761A pdb=" N CYS A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.537A pdb=" N VAL A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 182 " --> pdb=" O MET A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.542A pdb=" N LYS A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.567A pdb=" N THR A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 275 removed outlier: 3.729A pdb=" N TYR A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 292 removed outlier: 3.554A pdb=" N GLU A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 796 Processing helix chain 'A' and resid 800 through 823 removed outlier: 3.569A pdb=" N LEU A 804 " --> pdb=" O ASN A 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 49 removed outlier: 3.846A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.859A pdb=" N VAL B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 removed outlier: 3.605A pdb=" N ALA B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.828A pdb=" N HIS B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 170 removed outlier: 3.761A pdb=" N CYS B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.535A pdb=" N VAL B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.541A pdb=" N LYS B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.567A pdb=" N THR B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 275 removed outlier: 3.729A pdb=" N TYR B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.554A pdb=" N GLU B 292 " --> pdb=" O ASN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 796 Processing helix chain 'B' and resid 800 through 823 removed outlier: 3.568A pdb=" N LEU B 804 " --> pdb=" O ASN B 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 49 removed outlier: 3.847A pdb=" N TYR C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 61 Processing helix chain 'C' and resid 85 through 94 removed outlier: 3.860A pdb=" N VAL C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 112 removed outlier: 3.605A pdb=" N ALA C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.828A pdb=" N HIS C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 170 removed outlier: 3.761A pdb=" N CYS C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.536A pdb=" N VAL C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 182 " --> pdb=" O MET C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.541A pdb=" N LYS C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 233 through 252 removed outlier: 3.567A pdb=" N THR C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 275 removed outlier: 3.729A pdb=" N TYR C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 292 removed outlier: 3.555A pdb=" N GLU C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 796 Processing helix chain 'C' and resid 800 through 823 removed outlier: 3.569A pdb=" N LEU C 804 " --> pdb=" O ASN C 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 49 removed outlier: 3.846A pdb=" N TYR D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 85 through 94 removed outlier: 3.859A pdb=" N VAL D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 3.605A pdb=" N ALA D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.827A pdb=" N HIS D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 170 removed outlier: 3.761A pdb=" N CYS D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.535A pdb=" N VAL D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS D 182 " --> pdb=" O MET D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.542A pdb=" N LYS D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.566A pdb=" N THR D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 275 removed outlier: 3.729A pdb=" N TYR D 259 " --> pdb=" O PHE D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 292 removed outlier: 3.555A pdb=" N GLU D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 796 Processing helix chain 'D' and resid 800 through 823 removed outlier: 3.568A pdb=" N LEU D 804 " --> pdb=" O ASN D 800 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1503 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: 1.26 Time building geometry restraints manager: 1.14 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: 3084 1.34 - 1.46: 1532 1.46 - 1.58: 4588 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9288 Sorted by residual: bond pdb=" C SER A 158 " pdb=" N PRO A 159 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.44e-02 4.82e+03 4.09e+00 bond pdb=" C SER C 158 " pdb=" N PRO C 159 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.44e-02 4.82e+03 4.09e+00 bond pdb=" C SER D 158 " pdb=" N PRO D 159 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.44e-02 4.82e+03 4.09e+00 bond pdb=" C SER B 158 " pdb=" N PRO B 159 " ideal model delta sigma weight residual 1.326 1.355 -0.029 1.44e-02 4.82e+03 3.94e+00 bond pdb=" N PRO C 224 " pdb=" CD PRO C 224 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.44e+00 ... (remaining 9283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 11848 1.72 - 3.45: 496 3.45 - 5.17: 100 5.17 - 6.89: 24 6.89 - 8.62: 12 Bond angle restraints: 12480 Sorted by residual: angle pdb=" C GLU B 232 " pdb=" N ASP B 233 " pdb=" CA ASP B 233 " ideal model delta sigma weight residual 122.83 127.55 -4.72 1.08e+00 8.57e-01 1.91e+01 angle pdb=" C GLU D 232 " pdb=" N ASP D 233 " pdb=" CA ASP D 233 " ideal model delta sigma weight residual 122.83 127.52 -4.69 1.08e+00 8.57e-01 1.89e+01 angle pdb=" C GLU A 232 " pdb=" N ASP A 233 " pdb=" CA ASP A 233 " ideal model delta sigma weight residual 122.83 127.52 -4.69 1.08e+00 8.57e-01 1.89e+01 angle pdb=" C GLU C 232 " pdb=" N ASP C 233 " pdb=" CA ASP C 233 " ideal model delta sigma weight residual 122.83 127.50 -4.67 1.08e+00 8.57e-01 1.87e+01 angle pdb=" N HIS D 124 " pdb=" CA HIS D 124 " pdb=" C HIS D 124 " ideal model delta sigma weight residual 109.81 118.43 -8.62 2.21e+00 2.05e-01 1.52e+01 ... (remaining 12475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.43: 5112 9.43 - 18.85: 644 18.85 - 28.28: 24 28.28 - 37.71: 12 37.71 - 47.14: 12 Dihedral angle restraints: 5804 sinusoidal: 2412 harmonic: 3392 Sorted by residual: dihedral pdb=" CA SER C 158 " pdb=" C SER C 158 " pdb=" N PRO C 159 " pdb=" CA PRO C 159 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER D 158 " pdb=" C SER D 158 " pdb=" N PRO D 159 " pdb=" CA PRO D 159 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER A 158 " pdb=" C SER A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 5801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 925 0.044 - 0.088: 382 0.088 - 0.132: 82 0.132 - 0.177: 25 0.177 - 0.221: 6 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA HIS C 124 " pdb=" N HIS C 124 " pdb=" C HIS C 124 " pdb=" CB HIS C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA HIS A 124 " pdb=" N HIS A 124 " pdb=" C HIS A 124 " pdb=" CB HIS A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA HIS B 124 " pdb=" N HIS B 124 " pdb=" C HIS B 124 " pdb=" CB HIS B 124 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1417 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 158 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 159 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 233 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO D 234 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 234 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 234 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 158 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO C 159 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 159 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 159 " -0.027 5.00e-02 4.00e+02 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2323 2.80 - 3.32: 8416 3.32 - 3.85: 13449 3.85 - 4.37: 16353 4.37 - 4.90: 26973 Nonbonded interactions: 67514 Sorted by model distance: nonbonded pdb=" O VAL C 82 " pdb=" OH TYR C 114 " model vdw 2.273 3.040 nonbonded pdb=" O VAL B 82 " pdb=" OH TYR B 114 " model vdw 2.273 3.040 nonbonded pdb=" O VAL A 82 " pdb=" OH TYR A 114 " model vdw 2.273 3.040 nonbonded pdb=" O VAL D 82 " pdb=" OH TYR D 114 " model vdw 2.273 3.040 nonbonded pdb=" NZ LYS A 808 " pdb=" OE1 GLU D 806 " model vdw 2.299 3.120 ... (remaining 67509 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.130 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.500 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 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 0.064 9288 Z= 0.203 Angle : 0.861 8.617 12480 Z= 0.488 Chirality : 0.052 0.221 1420 Planarity : 0.005 0.048 1612 Dihedral : 7.646 47.136 3596 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.18), residues: 1128 helix: -1.64 (0.14), residues: 780 sheet: None (None), residues: 0 loop : -4.70 (0.21), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 785 TYR 0.014 0.002 TYR C 218 PHE 0.010 0.002 PHE A 193 HIS 0.005 0.002 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 ( 9288) covalent geometry : angle 0.86103 / 0.49 (12480) hydrogen bonds : bond 0.07609 / 4.83 ( 509) hydrogen bonds : angle 5.44504 / 3.88 ( 1503) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.7401 (mt) cc_final: 0.6854 (mp) REVERT: A 72 TYR cc_start: 0.6655 (m-80) cc_final: 0.5769 (m-80) REVERT: A 221 LEU cc_start: 0.8458 (mt) cc_final: 0.8241 (tp) REVERT: A 245 LEU cc_start: 0.9359 (mt) cc_final: 0.9147 (mt) REVERT: A 793 ASP cc_start: 0.8785 (m-30) cc_final: 0.8447 (t0) REVERT: A 822 LYS cc_start: 0.8562 (mttt) cc_final: 0.8318 (tppt) REVERT: B 65 LEU cc_start: 0.7305 (mt) cc_final: 0.6748 (mp) REVERT: B 72 TYR cc_start: 0.6631 (m-80) cc_final: 0.6168 (m-80) REVERT: B 221 LEU cc_start: 0.8465 (mt) cc_final: 0.8212 (tp) REVERT: B 245 LEU cc_start: 0.9361 (mt) cc_final: 0.9145 (mt) REVERT: B 793 ASP cc_start: 0.8783 (m-30) cc_final: 0.8454 (t0) REVERT: C 65 LEU cc_start: 0.7303 (mt) cc_final: 0.6751 (mp) REVERT: C 72 TYR cc_start: 0.6667 (m-80) cc_final: 0.6106 (m-80) REVERT: C 221 LEU cc_start: 0.8463 (mt) cc_final: 0.8244 (tp) REVERT: C 245 LEU cc_start: 0.9382 (mt) cc_final: 0.9167 (mt) REVERT: C 793 ASP cc_start: 0.8783 (m-30) cc_final: 0.8424 (t0) REVERT: D 65 LEU cc_start: 0.7404 (mt) cc_final: 0.6856 (mp) REVERT: D 72 TYR cc_start: 0.6656 (m-80) cc_final: 0.6123 (m-80) REVERT: D 221 LEU cc_start: 0.8459 (mt) cc_final: 0.8237 (tp) REVERT: D 245 LEU cc_start: 0.9362 (mt) cc_final: 0.9146 (mt) REVERT: D 793 ASP cc_start: 0.8781 (m-30) cc_final: 0.8451 (t0) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.1180 time to fit residues: 63.7391 Evaluate side-chains 231 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.0970 chunk 106 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 HIS A 177 HIS B 66 ASN B 75 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS B 177 HIS C 66 ASN C 75 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS C 177 HIS D 75 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS D 177 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.102852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.090708 restraints weight = 33827.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.092298 restraints weight = 24335.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.093487 restraints weight = 18845.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.094380 restraints weight = 15359.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.095046 restraints weight = 13029.927| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9288 Z= 0.152 Angle : 0.742 6.265 12480 Z= 0.386 Chirality : 0.043 0.139 1420 Planarity : 0.004 0.034 1612 Dihedral : 5.694 20.033 1248 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.25 % Allowed : 10.73 % Favored : 86.02 % 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: -2.17 (0.22), residues: 1128 helix: -0.08 (0.17), residues: 784 sheet: None (None), residues: 0 loop : -4.76 (0.20), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.010 0.001 TYR C 192 PHE 0.007 0.001 PHE D 43 HIS 0.005 0.001 HIS D 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 9288) covalent geometry : angle 0.74239 / 0.39 (12480) hydrogen bonds : bond 0.03457 / 2.22 ( 509) hydrogen bonds : angle 4.51551 / 3.21 ( 1503) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.6954 (tp30) cc_final: 0.6655 (tp30) REVERT: A 245 LEU cc_start: 0.9264 (mt) cc_final: 0.9063 (mt) REVERT: A 793 ASP cc_start: 0.8706 (m-30) cc_final: 0.8474 (t0) REVERT: A 817 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8111 (mt-10) REVERT: B 174 GLU cc_start: 0.6921 (tp30) cc_final: 0.6612 (tp30) REVERT: B 779 MET cc_start: 0.8972 (tpp) cc_final: 0.8547 (tpp) REVERT: B 793 ASP cc_start: 0.8675 (m-30) cc_final: 0.8458 (t0) REVERT: B 817 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8106 (mt-10) REVERT: C 174 GLU cc_start: 0.6903 (tp30) cc_final: 0.6590 (tp30) REVERT: C 793 ASP cc_start: 0.8691 (m-30) cc_final: 0.8463 (t0) REVERT: D 174 GLU cc_start: 0.6953 (tp30) cc_final: 0.6716 (tp30) REVERT: D 245 LEU cc_start: 0.9254 (mt) cc_final: 0.9051 (mt) REVERT: D 779 MET cc_start: 0.8977 (tpp) cc_final: 0.8553 (tpp) REVERT: D 793 ASP cc_start: 0.8706 (m-30) cc_final: 0.8482 (t0) outliers start: 33 outliers final: 11 residues processed: 253 average time/residue: 0.1009 time to fit residues: 34.8065 Evaluate side-chains 165 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 chunk 45 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 75 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN C 75 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN D 75 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.102522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.090703 restraints weight = 33641.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.092594 restraints weight = 22607.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.093943 restraints weight = 16546.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.094923 restraints weight = 12873.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.095579 restraints weight = 10535.068| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9288 Z= 0.161 Angle : 0.821 12.884 12480 Z= 0.408 Chirality : 0.046 0.262 1420 Planarity : 0.005 0.058 1612 Dihedral : 5.472 20.029 1248 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 2.95 % Allowed : 11.81 % Favored : 85.24 % 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: -1.50 (0.23), residues: 1128 helix: 0.49 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -4.71 (0.19), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 815 TYR 0.018 0.001 TYR A 49 PHE 0.004 0.001 PHE B 193 HIS 0.003 0.001 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9288) covalent geometry : angle 0.82118 / 0.41 (12480) hydrogen bonds : bond 0.03609 / 2.35 ( 509) hydrogen bonds : angle 4.46751 / 3.16 ( 1503) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8270 (pp30) REVERT: A 174 GLU cc_start: 0.7249 (tp30) cc_final: 0.6705 (tp30) REVERT: A 264 MET cc_start: 0.8607 (mmm) cc_final: 0.8229 (mmm) REVERT: A 793 ASP cc_start: 0.8730 (m-30) cc_final: 0.8373 (t0) REVERT: B 174 GLU cc_start: 0.7210 (tp30) cc_final: 0.6698 (tp30) REVERT: B 264 MET cc_start: 0.8585 (mmm) cc_final: 0.8211 (mmm) REVERT: B 793 ASP cc_start: 0.8712 (m-30) cc_final: 0.8365 (t0) REVERT: C 174 GLU cc_start: 0.7197 (tp30) cc_final: 0.6688 (tp30) REVERT: C 264 MET cc_start: 0.8612 (mmm) cc_final: 0.8241 (mmm) REVERT: C 793 ASP cc_start: 0.8722 (m-30) cc_final: 0.8364 (t0) REVERT: D 174 GLU cc_start: 0.7158 (tp30) cc_final: 0.6736 (tp30) REVERT: D 178 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7930 (ptm) REVERT: D 264 MET cc_start: 0.8608 (mmm) cc_final: 0.8233 (mmm) REVERT: D 793 ASP cc_start: 0.8727 (m-30) cc_final: 0.8377 (t0) outliers start: 30 outliers final: 8 residues processed: 198 average time/residue: 0.0726 time to fit residues: 21.5586 Evaluate side-chains 160 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 178 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 50 optimal weight: 2.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 75 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN C 75 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.103041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.091264 restraints weight = 33111.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.093034 restraints weight = 23065.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.094324 restraints weight = 17249.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.095281 restraints weight = 13656.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.095882 restraints weight = 11305.962| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9288 Z= 0.132 Angle : 0.772 11.413 12480 Z= 0.385 Chirality : 0.043 0.227 1420 Planarity : 0.005 0.065 1612 Dihedral : 5.242 19.062 1248 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 2.17 % Allowed : 12.60 % Favored : 85.24 % 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: -1.06 (0.24), residues: 1128 helix: 0.88 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -4.58 (0.21), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.015 0.001 TYR C 72 PHE 0.004 0.001 PHE D 193 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 9288) covalent geometry : angle 0.77155 / 0.39 (12480) hydrogen bonds : bond 0.03438 / 2.24 ( 509) hydrogen bonds : angle 4.37782 / 3.10 ( 1503) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 GLU cc_start: 0.7216 (tp30) cc_final: 0.6619 (tp30) REVERT: A 793 ASP cc_start: 0.8642 (m-30) cc_final: 0.8312 (t0) REVERT: A 794 LYS cc_start: 0.8897 (tptp) cc_final: 0.8501 (tppp) REVERT: B 174 GLU cc_start: 0.7164 (tp30) cc_final: 0.6577 (tp30) REVERT: B 245 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8957 (mm) REVERT: B 779 MET cc_start: 0.8961 (tpp) cc_final: 0.8642 (mpp) REVERT: B 793 ASP cc_start: 0.8606 (m-30) cc_final: 0.8361 (t0) REVERT: B 794 LYS cc_start: 0.8882 (tptp) cc_final: 0.8511 (tppp) REVERT: C 174 GLU cc_start: 0.7166 (tp30) cc_final: 0.6583 (tp30) REVERT: C 245 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8961 (mm) REVERT: C 779 MET cc_start: 0.8954 (tpp) cc_final: 0.8638 (mpp) REVERT: C 793 ASP cc_start: 0.8629 (m-30) cc_final: 0.8371 (t0) REVERT: C 794 LYS cc_start: 0.8892 (tptp) cc_final: 0.8505 (tppp) REVERT: D 116 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6478 (tpp80) REVERT: D 174 GLU cc_start: 0.7110 (tp30) cc_final: 0.6583 (tp30) REVERT: D 779 MET cc_start: 0.8937 (tpp) cc_final: 0.8645 (mpp) REVERT: D 793 ASP cc_start: 0.8669 (m-30) cc_final: 0.8400 (t0) REVERT: D 794 LYS cc_start: 0.8903 (tptp) cc_final: 0.8511 (tppp) outliers start: 22 outliers final: 11 residues processed: 197 average time/residue: 0.0659 time to fit residues: 19.5636 Evaluate side-chains 172 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 106 optimal weight: 0.0270 chunk 65 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN ** D 76 ASN ** 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 = 0.3885 r_free = 0.3885 target = 0.102879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.090747 restraints weight = 33536.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.092682 restraints weight = 22992.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.094049 restraints weight = 17051.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.095014 restraints weight = 13428.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.095901 restraints weight = 11115.863| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9288 Z= 0.135 Angle : 0.753 11.232 12480 Z= 0.375 Chirality : 0.043 0.192 1420 Planarity : 0.004 0.038 1612 Dihedral : 5.108 18.790 1248 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.87 % Allowed : 15.45 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.25), residues: 1128 helix: 1.12 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -4.35 (0.22), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 815 TYR 0.016 0.001 TYR A 72 PHE 0.006 0.001 PHE C 193 HIS 0.003 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 9288) covalent geometry : angle 0.75281 / 0.38 (12480) hydrogen bonds : bond 0.03341 / 2.19 ( 509) hydrogen bonds : angle 4.36351 / 3.03 ( 1503) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.9313 (mm) cc_final: 0.8834 (tt) REVERT: A 174 GLU cc_start: 0.7205 (tp30) cc_final: 0.6875 (tp30) REVERT: A 264 MET cc_start: 0.8380 (mmm) cc_final: 0.8071 (mmm) REVERT: A 793 ASP cc_start: 0.8689 (m-30) cc_final: 0.8435 (t0) REVERT: A 794 LYS cc_start: 0.8860 (tptp) cc_final: 0.8513 (tppp) REVERT: B 165 ILE cc_start: 0.9320 (mm) cc_final: 0.8839 (tt) REVERT: B 174 GLU cc_start: 0.7186 (tp30) cc_final: 0.6859 (tp30) REVERT: B 264 MET cc_start: 0.8382 (mmm) cc_final: 0.8090 (mmm) REVERT: B 793 ASP cc_start: 0.8652 (m-30) cc_final: 0.8405 (t0) REVERT: B 794 LYS cc_start: 0.8837 (tptp) cc_final: 0.8519 (tppp) REVERT: C 165 ILE cc_start: 0.9281 (mm) cc_final: 0.8797 (tt) REVERT: C 174 GLU cc_start: 0.7164 (tp30) cc_final: 0.6852 (tp30) REVERT: C 264 MET cc_start: 0.8403 (mmm) cc_final: 0.8104 (mmm) REVERT: C 793 ASP cc_start: 0.8664 (m-30) cc_final: 0.8411 (t0) REVERT: C 794 LYS cc_start: 0.8854 (tptp) cc_final: 0.8532 (tppp) REVERT: D 165 ILE cc_start: 0.9309 (mm) cc_final: 0.8843 (tt) REVERT: D 174 GLU cc_start: 0.7246 (tp30) cc_final: 0.6567 (tp30) REVERT: D 264 MET cc_start: 0.8395 (mmm) cc_final: 0.8090 (mmm) REVERT: D 793 ASP cc_start: 0.8694 (m-30) cc_final: 0.8430 (t0) REVERT: D 794 LYS cc_start: 0.8870 (tptp) cc_final: 0.8518 (tppp) outliers start: 19 outliers final: 10 residues processed: 212 average time/residue: 0.0686 time to fit residues: 21.8722 Evaluate side-chains 174 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 44 optimal weight: 0.0670 chunk 109 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN ** D 76 ASN ** 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 = 0.3861 r_free = 0.3861 target = 0.101532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.089285 restraints weight = 33851.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.091125 restraints weight = 23362.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.092481 restraints weight = 17393.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.093523 restraints weight = 13693.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.094283 restraints weight = 11275.747| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9288 Z= 0.140 Angle : 0.791 12.853 12480 Z= 0.393 Chirality : 0.045 0.245 1420 Planarity : 0.004 0.034 1612 Dihedral : 4.997 18.614 1248 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.95 % Allowed : 17.91 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.25), residues: 1128 helix: 1.22 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -4.38 (0.22), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 815 TYR 0.011 0.001 TYR B 72 PHE 0.004 0.001 PHE B 193 HIS 0.003 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9288) covalent geometry : angle 0.79100 / 0.39 (12480) hydrogen bonds : bond 0.03404 / 2.26 ( 509) hydrogen bonds : angle 4.34037 / 3.05 ( 1503) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.9344 (mm) cc_final: 0.8891 (tt) REVERT: A 174 GLU cc_start: 0.7253 (tp30) cc_final: 0.6920 (tp30) REVERT: A 264 MET cc_start: 0.8463 (mmm) cc_final: 0.8218 (mmm) REVERT: A 793 ASP cc_start: 0.8714 (m-30) cc_final: 0.8450 (t0) REVERT: A 794 LYS cc_start: 0.8796 (tptp) cc_final: 0.8532 (tppp) REVERT: B 165 ILE cc_start: 0.9353 (mm) cc_final: 0.8890 (tt) REVERT: B 174 GLU cc_start: 0.7218 (tp30) cc_final: 0.6901 (tp30) REVERT: B 264 MET cc_start: 0.8457 (mmm) cc_final: 0.8217 (mmm) REVERT: B 793 ASP cc_start: 0.8652 (m-30) cc_final: 0.8431 (t0) REVERT: C 165 ILE cc_start: 0.9352 (mm) cc_final: 0.8889 (tt) REVERT: C 174 GLU cc_start: 0.7221 (tp30) cc_final: 0.6914 (tp30) REVERT: C 264 MET cc_start: 0.8478 (mmm) cc_final: 0.8214 (mmm) REVERT: C 793 ASP cc_start: 0.8676 (m-30) cc_final: 0.8434 (t0) REVERT: D 165 ILE cc_start: 0.9340 (mm) cc_final: 0.8896 (tt) REVERT: D 174 GLU cc_start: 0.7260 (tp30) cc_final: 0.6837 (tp30) REVERT: D 264 MET cc_start: 0.8459 (mmm) cc_final: 0.8221 (mmm) REVERT: D 793 ASP cc_start: 0.8716 (m-30) cc_final: 0.8460 (t0) outliers start: 30 outliers final: 13 residues processed: 198 average time/residue: 0.0699 time to fit residues: 20.8823 Evaluate side-chains 176 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 0.0270 chunk 56 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 75 GLN ** D 76 ASN ** 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 = 0.3888 r_free = 0.3888 target = 0.102849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.090754 restraints weight = 33946.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.092681 restraints weight = 23006.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.094083 restraints weight = 16990.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.095057 restraints weight = 13336.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.095824 restraints weight = 10971.651| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.6463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9288 Z= 0.140 Angle : 0.813 13.835 12480 Z= 0.404 Chirality : 0.044 0.176 1420 Planarity : 0.004 0.033 1612 Dihedral : 4.892 19.018 1248 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.36 % Allowed : 18.01 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.25), residues: 1128 helix: 1.28 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -4.37 (0.21), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 116 TYR 0.018 0.001 TYR A 72 PHE 0.007 0.001 PHE B 193 HIS 0.003 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9288) covalent geometry : angle 0.81331 / 0.40 (12480) hydrogen bonds : bond 0.03235 / 2.13 ( 509) hydrogen bonds : angle 4.29789 / 3.01 ( 1503) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.9369 (mm) cc_final: 0.8886 (tt) REVERT: A 174 GLU cc_start: 0.7322 (tp30) cc_final: 0.6926 (tp30) REVERT: A 264 MET cc_start: 0.8424 (mmm) cc_final: 0.8213 (mmm) REVERT: A 793 ASP cc_start: 0.8682 (m-30) cc_final: 0.8408 (t0) REVERT: A 794 LYS cc_start: 0.8836 (tptp) cc_final: 0.8469 (tppp) REVERT: A 795 GLU cc_start: 0.8284 (mp0) cc_final: 0.7913 (mp0) REVERT: B 165 ILE cc_start: 0.9354 (mm) cc_final: 0.8886 (tt) REVERT: B 174 GLU cc_start: 0.7332 (tp30) cc_final: 0.6934 (tp30) REVERT: B 264 MET cc_start: 0.8402 (mmm) cc_final: 0.8162 (mmm) REVERT: B 793 ASP cc_start: 0.8637 (m-30) cc_final: 0.8370 (t0) REVERT: B 794 LYS cc_start: 0.8910 (tptp) cc_final: 0.8416 (tppp) REVERT: B 795 GLU cc_start: 0.8307 (mp0) cc_final: 0.7842 (mp0) REVERT: C 165 ILE cc_start: 0.9366 (mm) cc_final: 0.8899 (tt) REVERT: C 174 GLU cc_start: 0.7350 (tp30) cc_final: 0.6940 (tp30) REVERT: C 264 MET cc_start: 0.8462 (mmm) cc_final: 0.8246 (mmm) REVERT: C 793 ASP cc_start: 0.8638 (m-30) cc_final: 0.8364 (t0) REVERT: C 794 LYS cc_start: 0.8912 (tptp) cc_final: 0.8396 (tppp) REVERT: C 795 GLU cc_start: 0.8310 (mp0) cc_final: 0.7840 (mp0) REVERT: D 165 ILE cc_start: 0.9367 (mm) cc_final: 0.8884 (tt) REVERT: D 174 GLU cc_start: 0.7292 (tp30) cc_final: 0.6954 (tp30) REVERT: D 264 MET cc_start: 0.8444 (mmm) cc_final: 0.8234 (mmm) REVERT: D 793 ASP cc_start: 0.8650 (m-30) cc_final: 0.8372 (t0) REVERT: D 794 LYS cc_start: 0.8915 (tptp) cc_final: 0.8393 (tppp) REVERT: D 795 GLU cc_start: 0.8314 (mp0) cc_final: 0.7843 (mp0) outliers start: 24 outliers final: 14 residues processed: 199 average time/residue: 0.0832 time to fit residues: 24.0897 Evaluate side-chains 178 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 100 optimal weight: 0.0010 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 42 optimal weight: 0.0870 chunk 40 optimal weight: 0.1980 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.103472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.091921 restraints weight = 32889.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.093673 restraints weight = 23025.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.094943 restraints weight = 17391.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.095849 restraints weight = 13886.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.096551 restraints weight = 11570.853| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9288 Z= 0.141 Angle : 0.828 13.799 12480 Z= 0.409 Chirality : 0.045 0.249 1420 Planarity : 0.004 0.031 1612 Dihedral : 4.844 17.236 1248 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 1.77 % Allowed : 19.49 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.25), residues: 1128 helix: 1.29 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -4.33 (0.22), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 188 TYR 0.011 0.001 TYR C 72 PHE 0.004 0.001 PHE B 193 HIS 0.003 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 9288) covalent geometry : angle 0.82795 / 0.41 (12480) hydrogen bonds : bond 0.03192 / 2.10 ( 509) hydrogen bonds : angle 4.27029 / 2.99 ( 1503) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.9275 (mm) cc_final: 0.8852 (tt) REVERT: A 174 GLU cc_start: 0.7201 (tp30) cc_final: 0.6857 (tp30) REVERT: A 793 ASP cc_start: 0.8621 (m-30) cc_final: 0.8397 (t0) REVERT: A 794 LYS cc_start: 0.8777 (tptp) cc_final: 0.8523 (tppp) REVERT: B 165 ILE cc_start: 0.9276 (mm) cc_final: 0.8852 (tt) REVERT: B 174 GLU cc_start: 0.7243 (tp30) cc_final: 0.6888 (tp30) REVERT: B 793 ASP cc_start: 0.8563 (m-30) cc_final: 0.8347 (t0) REVERT: B 794 LYS cc_start: 0.8829 (tptp) cc_final: 0.8457 (tppp) REVERT: C 165 ILE cc_start: 0.9271 (mm) cc_final: 0.8844 (tt) REVERT: C 174 GLU cc_start: 0.7234 (tp30) cc_final: 0.6879 (tp30) REVERT: C 793 ASP cc_start: 0.8567 (m-30) cc_final: 0.8348 (t0) REVERT: C 794 LYS cc_start: 0.8829 (tptp) cc_final: 0.8441 (tppp) REVERT: D 165 ILE cc_start: 0.9272 (mm) cc_final: 0.8850 (tt) REVERT: D 174 GLU cc_start: 0.7113 (tp30) cc_final: 0.6805 (tp30) REVERT: D 793 ASP cc_start: 0.8584 (m-30) cc_final: 0.8359 (t0) REVERT: D 794 LYS cc_start: 0.8857 (tptp) cc_final: 0.8468 (tppp) outliers start: 18 outliers final: 16 residues processed: 183 average time/residue: 0.0831 time to fit residues: 22.1941 Evaluate side-chains 179 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.0060 chunk 15 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.100217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.088127 restraints weight = 34457.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.089872 restraints weight = 24127.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091136 restraints weight = 18221.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.092138 restraints weight = 14537.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.092857 restraints weight = 12017.680| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9288 Z= 0.160 Angle : 0.850 14.101 12480 Z= 0.424 Chirality : 0.046 0.270 1420 Planarity : 0.004 0.033 1612 Dihedral : 4.909 24.538 1248 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 1.77 % Allowed : 21.16 % Favored : 77.07 % 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: -0.38 (0.26), residues: 1128 helix: 1.35 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -4.42 (0.22), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 188 TYR 0.014 0.001 TYR A 72 PHE 0.009 0.001 PHE A 193 HIS 0.004 0.001 HIS D 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 9288) covalent geometry : angle 0.85006 / 0.42 (12480) hydrogen bonds : bond 0.03420 / 2.24 ( 509) hydrogen bonds : angle 4.34094 / 3.03 ( 1503) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.9354 (mm) cc_final: 0.8926 (tt) REVERT: A 174 GLU cc_start: 0.7203 (tp30) cc_final: 0.6887 (tp30) REVERT: A 793 ASP cc_start: 0.8727 (m-30) cc_final: 0.8482 (t0) REVERT: A 794 LYS cc_start: 0.8859 (tptp) cc_final: 0.8629 (tptm) REVERT: A 795 GLU cc_start: 0.8302 (mp0) cc_final: 0.7938 (mp0) REVERT: B 165 ILE cc_start: 0.9358 (mm) cc_final: 0.8934 (tt) REVERT: B 174 GLU cc_start: 0.7206 (tp30) cc_final: 0.6883 (tp30) REVERT: B 793 ASP cc_start: 0.8691 (m-30) cc_final: 0.8428 (t0) REVERT: B 794 LYS cc_start: 0.8803 (tptp) cc_final: 0.8441 (tppp) REVERT: B 795 GLU cc_start: 0.8398 (mp0) cc_final: 0.8013 (mp0) REVERT: C 165 ILE cc_start: 0.9347 (mm) cc_final: 0.8926 (tt) REVERT: C 174 GLU cc_start: 0.7202 (tp30) cc_final: 0.6878 (tp30) REVERT: C 793 ASP cc_start: 0.8678 (m-30) cc_final: 0.8402 (t0) REVERT: C 794 LYS cc_start: 0.8807 (tptp) cc_final: 0.8416 (tppp) REVERT: C 795 GLU cc_start: 0.8394 (mp0) cc_final: 0.8022 (mp0) REVERT: D 165 ILE cc_start: 0.9347 (mm) cc_final: 0.8931 (tt) REVERT: D 174 GLU cc_start: 0.7213 (tp30) cc_final: 0.6899 (tp30) REVERT: D 793 ASP cc_start: 0.8708 (m-30) cc_final: 0.8457 (t0) REVERT: D 794 LYS cc_start: 0.8813 (tptp) cc_final: 0.8415 (tppp) REVERT: D 795 GLU cc_start: 0.8432 (mp0) cc_final: 0.8016 (mp0) outliers start: 18 outliers final: 16 residues processed: 183 average time/residue: 0.0693 time to fit residues: 19.2408 Evaluate side-chains 173 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.0770 chunk 15 optimal weight: 0.0770 chunk 21 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 68 optimal weight: 0.0070 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 30 optimal weight: 6.9990 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN D 75 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.102716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.090509 restraints weight = 33745.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.092446 restraints weight = 23112.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.093880 restraints weight = 17139.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.094936 restraints weight = 13399.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.095685 restraints weight = 10990.085| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.6810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9288 Z= 0.145 Angle : 0.874 14.676 12480 Z= 0.428 Chirality : 0.046 0.294 1420 Planarity : 0.004 0.032 1612 Dihedral : 4.789 23.610 1248 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.17 % Allowed : 21.46 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.25), residues: 1128 helix: 1.59 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -4.20 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 188 TYR 0.014 0.001 TYR C 72 PHE 0.013 0.001 PHE A 269 HIS 0.003 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 9288) covalent geometry : angle 0.87398 / 0.43 (12480) hydrogen bonds : bond 0.03220 / 2.11 ( 509) hydrogen bonds : angle 4.18849 / 2.93 ( 1503) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ILE cc_start: 0.9348 (mm) cc_final: 0.8949 (tt) REVERT: A 174 GLU cc_start: 0.7260 (tp30) cc_final: 0.6890 (tp30) REVERT: B 165 ILE cc_start: 0.9353 (mm) cc_final: 0.8953 (tt) REVERT: B 174 GLU cc_start: 0.7299 (tp30) cc_final: 0.6923 (tp30) REVERT: B 791 GLN cc_start: 0.9013 (mt0) cc_final: 0.8429 (mt0) REVERT: B 793 ASP cc_start: 0.8609 (m-30) cc_final: 0.8338 (t0) REVERT: B 794 LYS cc_start: 0.8825 (tptp) cc_final: 0.8366 (tppp) REVERT: B 795 GLU cc_start: 0.8411 (mp0) cc_final: 0.7950 (mp0) REVERT: C 165 ILE cc_start: 0.9344 (mm) cc_final: 0.8884 (tt) REVERT: C 174 GLU cc_start: 0.7280 (tp30) cc_final: 0.6904 (tp30) REVERT: C 793 ASP cc_start: 0.8613 (m-30) cc_final: 0.8338 (t0) REVERT: C 794 LYS cc_start: 0.8832 (tptp) cc_final: 0.8376 (tppp) REVERT: C 795 GLU cc_start: 0.8407 (mp0) cc_final: 0.7986 (mp0) REVERT: D 165 ILE cc_start: 0.9340 (mm) cc_final: 0.8951 (tt) REVERT: D 174 GLU cc_start: 0.7309 (tp30) cc_final: 0.7018 (tp30) REVERT: D 791 GLN cc_start: 0.9049 (mt0) cc_final: 0.8481 (mt0) REVERT: D 793 ASP cc_start: 0.8635 (m-30) cc_final: 0.8356 (t0) REVERT: D 794 LYS cc_start: 0.8834 (tptp) cc_final: 0.8353 (tppp) REVERT: D 795 GLU cc_start: 0.8476 (mp0) cc_final: 0.8013 (mp0) outliers start: 22 outliers final: 16 residues processed: 192 average time/residue: 0.0738 time to fit residues: 21.3495 Evaluate side-chains 178 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain C residue 84 ASN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 788 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 100 optimal weight: 0.0270 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 800 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 800 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.102597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.090426 restraints weight = 33249.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.092344 restraints weight = 22694.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.093720 restraints weight = 16778.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.094710 restraints weight = 13173.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.095475 restraints weight = 10855.040| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.403 9288 Z= 0.458 Angle : 1.440 59.195 12480 Z= 0.879 Chirality : 0.073 1.349 1420 Planarity : 0.007 0.229 1612 Dihedral : 4.928 28.745 1248 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.60 % Favored : 91.22 % Rotamer: Outliers : 1.57 % Allowed : 22.34 % Favored : 76.08 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1128 helix: 1.53 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -4.23 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 188 TYR 0.014 0.001 TYR D 192 PHE 0.012 0.001 PHE A 269 HIS 0.003 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00907 / 0.46 ( 9288) covalent geometry : angle 1.44008 / 0.88 (12480) hydrogen bonds : bond 0.03266 / 2.15 ( 509) hydrogen bonds : angle 4.20738 / 2.94 ( 1503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1398.39 seconds wall clock time: 25 minutes 46.37 seconds (1546.37 seconds total)