Starting phenix.real_space_refine on Tue Mar 3 12:22:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlr_27512/03_2026/8dlr_27512.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlr_27512/03_2026/8dlr_27512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlr_27512/03_2026/8dlr_27512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlr_27512/03_2026/8dlr_27512.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlr_27512/03_2026/8dlr_27512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlr_27512/03_2026/8dlr_27512.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 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 16 5.16 5 C 2567 2.51 5 N 656 2.21 5 O 788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4027 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2218 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 14, 'TRANS': 259} Chain breaks: 2 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 937 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.11, per 1000 atoms: 0.28 Number of scatterers: 4027 At special positions: 0 Unit cell: (92, 64, 108, 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 16 16.00 O 788 8.00 N 656 7.00 C 2567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 149 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 282 " Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 210.2 milliseconds 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 7.9% alpha, 56.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.696A pdb=" N SER H 49 " --> pdb=" O GLY H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.966A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 129 removed outlier: 4.142A pdb=" N LYS H 127 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 50 Processing helix chain 'L' and resid 98 through 102 removed outlier: 4.143A pdb=" N GLU L 102 " --> pdb=" O ALA L 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.012A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.979A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.663A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.146A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N TYR A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N PHE A 157 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 12.835A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 11.146A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N TYR A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N PHE A 157 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.318A pdb=" N GLU H 29 " --> pdb=" O THR H 141 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE H 53 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG H 69 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.318A pdb=" N GLU H 29 " --> pdb=" O THR H 141 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL H 133 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 24 through 25 Processing sheet with id=AA9, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.403A pdb=" N TRP L 54 " --> pdb=" O VAL L 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 29 through 32 165 hydrogen bonds defined for protein. 405 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.63 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1253 1.34 - 1.47: 1107 1.47 - 1.59: 1744 1.59 - 1.71: 0 1.71 - 1.84: 21 Bond restraints: 4125 Sorted by residual: bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.93e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.67e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 4120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 5349 1.80 - 3.59: 228 3.59 - 5.39: 26 5.39 - 7.19: 3 7.19 - 8.98: 3 Bond angle restraints: 5609 Sorted by residual: angle pdb=" C GLN L 69 " pdb=" N ASP L 70 " pdb=" CA ASP L 70 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" CA ASN A 280 " pdb=" CB ASN A 280 " pdb=" CG ASN A 280 " ideal model delta sigma weight residual 112.60 115.46 -2.86 1.00e+00 1.00e+00 8.16e+00 angle pdb=" N GLY H 75 " pdb=" CA GLY H 75 " pdb=" C GLY H 75 " ideal model delta sigma weight residual 113.18 119.45 -6.27 2.37e+00 1.78e-01 7.00e+00 angle pdb=" N ASP A 287 " pdb=" CA ASP A 287 " pdb=" C ASP A 287 " ideal model delta sigma weight residual 108.79 104.81 3.98 1.53e+00 4.27e-01 6.76e+00 angle pdb=" CA LEU H 74 " pdb=" CB LEU H 74 " pdb=" CG LEU H 74 " ideal model delta sigma weight residual 116.30 125.28 -8.98 3.50e+00 8.16e-02 6.59e+00 ... (remaining 5604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 2293 16.63 - 33.26: 163 33.26 - 49.90: 32 49.90 - 66.53: 6 66.53 - 83.16: 8 Dihedral angle restraints: 2502 sinusoidal: 1038 harmonic: 1464 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -41.28 -44.72 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CA VAL A 90 " pdb=" C VAL A 90 " pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU H 74 " pdb=" C LEU H 74 " pdb=" N GLY H 75 " pdb=" CA GLY H 75 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 466 0.054 - 0.109: 135 0.109 - 0.163: 34 0.163 - 0.217: 3 0.217 - 0.271: 3 Chirality restraints: 641 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB THR A 63 " pdb=" CA THR A 63 " pdb=" OG1 THR A 63 " pdb=" CG2 THR A 63 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL A 227 " pdb=" CA VAL A 227 " pdb=" CG1 VAL A 227 " pdb=" CG2 VAL A 227 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 638 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO A 295 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 229 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO A 230 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 48 " -0.014 2.00e-02 2.50e+03 1.35e-02 3.20e+00 pdb=" CG PHE H 48 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 48 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE H 48 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 48 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 48 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE H 48 " -0.001 2.00e-02 2.50e+03 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1131 2.81 - 3.33: 3161 3.33 - 3.86: 6983 3.86 - 4.38: 8076 4.38 - 4.90: 14213 Nonbonded interactions: 33564 Sorted by model distance: nonbonded pdb=" OH TYR A 144 " pdb=" OH TYR H 129 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR H 52 " pdb=" O THR H 120 " model vdw 2.320 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OG1 THR A 114 " model vdw 2.342 3.040 nonbonded pdb=" O ASP L 111 " pdb=" OG1 THR L 114 " model vdw 2.346 3.040 nonbonded pdb=" NE2 GLN A 14 " pdb=" O TYR A 160 " model vdw 2.347 3.120 ... (remaining 33559 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.210 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4136 Z= 0.281 Angle : 0.834 8.983 5637 Z= 0.444 Chirality : 0.057 0.271 641 Planarity : 0.007 0.070 705 Dihedral : 12.705 83.158 1551 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -0.80 (0.36), residues: 495 helix: -0.46 (1.50), residues: 11 sheet: -0.36 (0.33), residues: 221 loop : -0.59 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 246 TYR 0.017 0.002 TYR H 79 PHE 0.030 0.003 PHE H 48 TRP 0.009 0.001 TRP H 66 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 4125) covalent geometry : angle 0.81081 ( 5609) SS BOND : bond 0.00469 ( 5) SS BOND : angle 1.85266 ( 10) hydrogen bonds : bond 0.13212 ( 150) hydrogen bonds : angle 6.94746 ( 405) link_NAG-ASN : bond 0.00442 ( 6) link_NAG-ASN : angle 3.35917 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.166 Fit side-chains REVERT: H 86 ARG cc_start: 0.8319 (mtp180) cc_final: 0.8006 (ttt180) REVERT: L 88 ASN cc_start: 0.8039 (m-40) cc_final: 0.7835 (m110) REVERT: L 102 GLU cc_start: 0.8303 (tt0) cc_final: 0.8042 (tt0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.5673 time to fit residues: 48.6011 Evaluate side-chains 70 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 207 HIS L 85 ASN L 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.101534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.075350 restraints weight = 6321.900| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.52 r_work: 0.2876 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4136 Z= 0.156 Angle : 0.564 6.540 5637 Z= 0.294 Chirality : 0.045 0.241 641 Planarity : 0.005 0.049 705 Dihedral : 6.580 56.396 670 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.92 % Allowed : 8.26 % Favored : 90.83 % 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: -0.55 (0.37), residues: 495 helix: -1.40 (1.23), residues: 17 sheet: -0.14 (0.34), residues: 210 loop : -0.38 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.010 0.001 TYR L 105 PHE 0.013 0.001 PHE A 175 TRP 0.004 0.001 TRP H 134 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4125) covalent geometry : angle 0.54606 ( 5609) SS BOND : bond 0.00319 ( 5) SS BOND : angle 1.17884 ( 10) hydrogen bonds : bond 0.02951 ( 150) hydrogen bonds : angle 5.70195 ( 405) link_NAG-ASN : bond 0.00267 ( 6) link_NAG-ASN : angle 2.44664 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.107 Fit side-chains REVERT: A 154 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8650 (mt-10) REVERT: H 82 LYS cc_start: 0.9051 (tmtt) cc_final: 0.8752 (tmtm) REVERT: H 86 ARG cc_start: 0.8302 (mtp180) cc_final: 0.7875 (ttt180) REVERT: H 106 ARG cc_start: 0.8422 (mtt180) cc_final: 0.8186 (mtt180) REVERT: L 88 ASN cc_start: 0.8144 (m-40) cc_final: 0.7799 (m110) REVERT: L 102 GLU cc_start: 0.8746 (tt0) cc_final: 0.8354 (tt0) outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.5516 time to fit residues: 42.1649 Evaluate side-chains 63 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN L 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.071741 restraints weight = 6048.552| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.61 r_work: 0.2763 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4136 Z= 0.220 Angle : 0.580 5.603 5637 Z= 0.302 Chirality : 0.046 0.244 641 Planarity : 0.004 0.043 705 Dihedral : 6.454 52.157 670 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.38 % Allowed : 9.86 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.37), residues: 495 helix: -0.98 (1.35), residues: 17 sheet: -0.02 (0.35), residues: 203 loop : -0.30 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.011 0.001 TYR L 105 PHE 0.019 0.002 PHE A 175 TRP 0.006 0.001 TRP H 66 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 4125) covalent geometry : angle 0.56185 ( 5609) SS BOND : bond 0.00366 ( 5) SS BOND : angle 1.25314 ( 10) hydrogen bonds : bond 0.03154 ( 150) hydrogen bonds : angle 5.61802 ( 405) link_NAG-ASN : bond 0.00199 ( 6) link_NAG-ASN : angle 2.47686 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.190 Fit side-chains REVERT: A 52 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8170 (tp40) REVERT: A 154 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8692 (mt-10) REVERT: H 25 GLN cc_start: 0.9214 (mt0) cc_final: 0.8964 (mt0) REVERT: H 82 LYS cc_start: 0.9016 (tmtt) cc_final: 0.8676 (tmtm) REVERT: H 86 ARG cc_start: 0.8354 (mtp180) cc_final: 0.7960 (ttp-170) REVERT: H 106 ARG cc_start: 0.8395 (mtt180) cc_final: 0.8072 (mtt180) REVERT: L 23 GLU cc_start: 0.8346 (pp20) cc_final: 0.8107 (pp20) REVERT: L 88 ASN cc_start: 0.8282 (m-40) cc_final: 0.7912 (m110) REVERT: L 102 GLU cc_start: 0.8781 (tt0) cc_final: 0.8509 (tt0) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.6238 time to fit residues: 44.3337 Evaluate side-chains 68 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.0570 chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.100587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.074177 restraints weight = 6276.054| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.53 r_work: 0.2852 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4136 Z= 0.178 Angle : 0.572 7.442 5637 Z= 0.298 Chirality : 0.044 0.232 641 Planarity : 0.004 0.041 705 Dihedral : 6.278 49.125 670 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.83 % Allowed : 11.01 % Favored : 87.16 % 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: -0.40 (0.37), residues: 495 helix: -0.75 (1.39), residues: 17 sheet: -0.06 (0.36), residues: 194 loop : -0.29 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.010 0.001 TYR A 269 PHE 0.015 0.001 PHE A 175 TRP 0.007 0.001 TRP H 66 HIS 0.001 0.000 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 4125) covalent geometry : angle 0.54701 ( 5609) SS BOND : bond 0.00320 ( 5) SS BOND : angle 2.41216 ( 10) hydrogen bonds : bond 0.02880 ( 150) hydrogen bonds : angle 5.46988 ( 405) link_NAG-ASN : bond 0.00237 ( 6) link_NAG-ASN : angle 2.42838 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8127 (tp40) REVERT: H 25 GLN cc_start: 0.9213 (mt0) cc_final: 0.8960 (mt0) REVERT: H 82 LYS cc_start: 0.9011 (tmtt) cc_final: 0.8766 (tmtm) REVERT: H 86 ARG cc_start: 0.8366 (mtp180) cc_final: 0.7954 (ttm170) REVERT: L 23 GLU cc_start: 0.8297 (pp20) cc_final: 0.8063 (pp20) REVERT: L 88 ASN cc_start: 0.8170 (m-40) cc_final: 0.7865 (m110) REVERT: L 102 GLU cc_start: 0.8736 (tt0) cc_final: 0.8280 (tt0) outliers start: 8 outliers final: 3 residues processed: 72 average time/residue: 0.6270 time to fit residues: 46.4772 Evaluate side-chains 67 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.071274 restraints weight = 6014.191| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.58 r_work: 0.2744 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 4136 Z= 0.214 Angle : 0.596 7.012 5637 Z= 0.309 Chirality : 0.045 0.239 641 Planarity : 0.004 0.041 705 Dihedral : 6.151 49.423 670 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.06 % Allowed : 12.16 % Favored : 85.78 % 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: -0.42 (0.37), residues: 495 helix: -0.64 (1.41), residues: 17 sheet: -0.12 (0.35), residues: 205 loop : -0.27 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 78 TYR 0.010 0.001 TYR A 269 PHE 0.018 0.002 PHE A 175 TRP 0.009 0.001 TRP H 66 HIS 0.001 0.000 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 4125) covalent geometry : angle 0.57280 ( 5609) SS BOND : bond 0.00429 ( 5) SS BOND : angle 2.29318 ( 10) hydrogen bonds : bond 0.03030 ( 150) hydrogen bonds : angle 5.47931 ( 405) link_NAG-ASN : bond 0.00229 ( 6) link_NAG-ASN : angle 2.45493 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.154 Fit side-chains REVERT: A 52 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8148 (tp40) REVERT: H 86 ARG cc_start: 0.8408 (mtp180) cc_final: 0.8041 (ttm170) REVERT: L 23 GLU cc_start: 0.8405 (pp20) cc_final: 0.8112 (pp20) REVERT: L 88 ASN cc_start: 0.8110 (m-40) cc_final: 0.7658 (m110) REVERT: L 102 GLU cc_start: 0.8752 (tt0) cc_final: 0.8308 (tt0) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.5824 time to fit residues: 41.5057 Evaluate side-chains 67 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 0.0050 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN H 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.072161 restraints weight = 6120.642| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.66 r_work: 0.2773 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4136 Z= 0.143 Angle : 0.559 7.513 5637 Z= 0.291 Chirality : 0.044 0.225 641 Planarity : 0.004 0.040 705 Dihedral : 5.779 49.203 670 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.06 % Allowed : 12.84 % Favored : 85.09 % 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: -0.27 (0.37), residues: 495 helix: -0.68 (1.37), residues: 17 sheet: -0.01 (0.35), residues: 202 loop : -0.17 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 78 TYR 0.009 0.001 TYR H 114 PHE 0.011 0.001 PHE A 175 TRP 0.006 0.001 TRP H 66 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4125) covalent geometry : angle 0.53597 ( 5609) SS BOND : bond 0.00321 ( 5) SS BOND : angle 2.14960 ( 10) hydrogen bonds : bond 0.02623 ( 150) hydrogen bonds : angle 5.30413 ( 405) link_NAG-ASN : bond 0.00263 ( 6) link_NAG-ASN : angle 2.38356 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.148 Fit side-chains REVERT: A 52 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8156 (tp40) REVERT: A 154 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8460 (mt-10) REVERT: H 67 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8055 (mtp) REVERT: H 86 ARG cc_start: 0.8488 (mtp180) cc_final: 0.7990 (ttm170) REVERT: H 127 LYS cc_start: 0.9108 (pttm) cc_final: 0.8852 (pttt) REVERT: L 88 ASN cc_start: 0.8078 (m-40) cc_final: 0.7668 (m110) REVERT: L 102 GLU cc_start: 0.8769 (tt0) cc_final: 0.8252 (mt-10) outliers start: 9 outliers final: 5 residues processed: 70 average time/residue: 0.6401 time to fit residues: 46.1427 Evaluate side-chains 70 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN H 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.099148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.071862 restraints weight = 6082.291| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.58 r_work: 0.2765 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4136 Z= 0.172 Angle : 0.579 8.654 5637 Z= 0.300 Chirality : 0.044 0.234 641 Planarity : 0.004 0.039 705 Dihedral : 5.755 49.700 670 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.06 % Allowed : 13.76 % Favored : 84.17 % 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: -0.42 (0.37), residues: 495 helix: -0.60 (1.39), residues: 17 sheet: -0.09 (0.34), residues: 205 loop : -0.30 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.010 0.001 TYR H 114 PHE 0.014 0.001 PHE A 175 TRP 0.007 0.001 TRP H 66 HIS 0.001 0.000 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 4125) covalent geometry : angle 0.55657 ( 5609) SS BOND : bond 0.00413 ( 5) SS BOND : angle 2.14188 ( 10) hydrogen bonds : bond 0.02761 ( 150) hydrogen bonds : angle 5.28498 ( 405) link_NAG-ASN : bond 0.00221 ( 6) link_NAG-ASN : angle 2.40993 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.126 Fit side-chains REVERT: A 52 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8130 (tp40) REVERT: A 154 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8529 (mt-10) REVERT: H 67 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7971 (mtp) REVERT: H 86 ARG cc_start: 0.8501 (mtp180) cc_final: 0.8050 (ttm170) REVERT: H 106 ARG cc_start: 0.8317 (mtt180) cc_final: 0.7829 (mtt180) REVERT: L 88 ASN cc_start: 0.8108 (m-40) cc_final: 0.7654 (m110) REVERT: L 102 GLU cc_start: 0.8766 (tt0) cc_final: 0.8233 (mt-10) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 0.5957 time to fit residues: 40.5959 Evaluate side-chains 66 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 0.0670 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.072352 restraints weight = 6022.462| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.63 r_work: 0.2777 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4136 Z= 0.151 Angle : 0.570 9.396 5637 Z= 0.295 Chirality : 0.044 0.229 641 Planarity : 0.004 0.038 705 Dihedral : 5.650 49.500 670 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.83 % Allowed : 13.53 % Favored : 84.63 % 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: -0.37 (0.37), residues: 495 helix: -0.59 (1.38), residues: 17 sheet: -0.07 (0.34), residues: 205 loop : -0.26 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 34 TYR 0.010 0.001 TYR H 114 PHE 0.013 0.001 PHE A 175 TRP 0.006 0.001 TRP H 66 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4125) covalent geometry : angle 0.54893 ( 5609) SS BOND : bond 0.00425 ( 5) SS BOND : angle 1.92476 ( 10) hydrogen bonds : bond 0.02657 ( 150) hydrogen bonds : angle 5.17792 ( 405) link_NAG-ASN : bond 0.00263 ( 6) link_NAG-ASN : angle 2.42602 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.150 Fit side-chains REVERT: A 52 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8152 (tp40) REVERT: A 154 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8441 (mt-10) REVERT: H 38 LYS cc_start: 0.8961 (tptm) cc_final: 0.8698 (tptm) REVERT: H 86 ARG cc_start: 0.8510 (mtp180) cc_final: 0.7989 (ttm170) REVERT: H 127 LYS cc_start: 0.9096 (pttm) cc_final: 0.8832 (pttt) REVERT: L 88 ASN cc_start: 0.8128 (m-40) cc_final: 0.7665 (m110) REVERT: L 102 GLU cc_start: 0.8701 (tt0) cc_final: 0.8179 (mt-10) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 0.6206 time to fit residues: 42.8511 Evaluate side-chains 69 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 25 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.072169 restraints weight = 6091.538| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.65 r_work: 0.2772 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4136 Z= 0.156 Angle : 0.565 8.869 5637 Z= 0.295 Chirality : 0.044 0.230 641 Planarity : 0.004 0.038 705 Dihedral : 5.642 49.672 670 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.61 % Allowed : 14.68 % Favored : 83.72 % 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: -0.35 (0.37), residues: 495 helix: -0.57 (1.38), residues: 17 sheet: -0.05 (0.35), residues: 205 loop : -0.25 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 80 TYR 0.010 0.001 TYR H 114 PHE 0.013 0.001 PHE A 175 TRP 0.012 0.001 TRP H 66 HIS 0.001 0.000 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4125) covalent geometry : angle 0.54478 ( 5609) SS BOND : bond 0.00447 ( 5) SS BOND : angle 1.82358 ( 10) hydrogen bonds : bond 0.02678 ( 150) hydrogen bonds : angle 5.15344 ( 405) link_NAG-ASN : bond 0.00226 ( 6) link_NAG-ASN : angle 2.40205 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.155 Fit side-chains REVERT: A 52 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8154 (tp40) REVERT: A 154 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8464 (mt-10) REVERT: H 67 MET cc_start: 0.8999 (mtm) cc_final: 0.8768 (mtp) REVERT: H 86 ARG cc_start: 0.8515 (mtp180) cc_final: 0.8171 (ttm170) REVERT: H 127 LYS cc_start: 0.9093 (pttm) cc_final: 0.8823 (pttt) REVERT: L 88 ASN cc_start: 0.8160 (m-40) cc_final: 0.7710 (m110) REVERT: L 102 GLU cc_start: 0.8750 (tt0) cc_final: 0.8265 (mt-10) outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 0.6398 time to fit residues: 43.4573 Evaluate side-chains 67 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 40 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.100931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.073441 restraints weight = 5951.925| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.60 r_work: 0.2794 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4136 Z= 0.131 Angle : 0.543 8.093 5637 Z= 0.283 Chirality : 0.044 0.225 641 Planarity : 0.004 0.038 705 Dihedral : 5.522 49.416 670 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.61 % Allowed : 14.45 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.37), residues: 495 helix: -0.54 (1.38), residues: 17 sheet: -0.03 (0.33), residues: 213 loop : -0.14 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 69 TYR 0.010 0.001 TYR H 114 PHE 0.010 0.001 PHE A 175 TRP 0.009 0.001 TRP H 66 HIS 0.001 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4125) covalent geometry : angle 0.52386 ( 5609) SS BOND : bond 0.00413 ( 5) SS BOND : angle 1.50990 ( 10) hydrogen bonds : bond 0.02498 ( 150) hydrogen bonds : angle 5.04034 ( 405) link_NAG-ASN : bond 0.00257 ( 6) link_NAG-ASN : angle 2.32714 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.162 Fit side-chains REVERT: A 52 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8128 (tp40) REVERT: A 154 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8399 (mt-10) REVERT: H 67 MET cc_start: 0.8912 (mtm) cc_final: 0.8675 (mtp) REVERT: H 86 ARG cc_start: 0.8456 (mtp180) cc_final: 0.8118 (ttm170) REVERT: H 127 LYS cc_start: 0.9070 (pttm) cc_final: 0.8815 (pttt) REVERT: L 88 ASN cc_start: 0.8150 (m-40) cc_final: 0.7706 (m110) REVERT: L 102 GLU cc_start: 0.8662 (tt0) cc_final: 0.8177 (mt-10) outliers start: 7 outliers final: 4 residues processed: 66 average time/residue: 0.6538 time to fit residues: 44.4455 Evaluate side-chains 67 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.070869 restraints weight = 6154.656| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.51 r_work: 0.2743 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4136 Z= 0.236 Angle : 0.608 8.793 5637 Z= 0.317 Chirality : 0.046 0.245 641 Planarity : 0.004 0.039 705 Dihedral : 5.866 49.665 670 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.38 % Allowed : 14.91 % Favored : 83.72 % 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: -0.37 (0.37), residues: 495 helix: -0.53 (1.40), residues: 17 sheet: -0.06 (0.35), residues: 205 loop : -0.28 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 69 TYR 0.012 0.001 TYR H 128 PHE 0.020 0.002 PHE A 175 TRP 0.013 0.001 TRP H 66 HIS 0.001 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 4125) covalent geometry : angle 0.58773 ( 5609) SS BOND : bond 0.00500 ( 5) SS BOND : angle 1.94830 ( 10) hydrogen bonds : bond 0.03079 ( 150) hydrogen bonds : angle 5.28630 ( 405) link_NAG-ASN : bond 0.00182 ( 6) link_NAG-ASN : angle 2.43567 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2086.72 seconds wall clock time: 36 minutes 15.56 seconds (2175.56 seconds total)