Starting phenix.real_space_refine on Wed Jul 23 19:24:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlr_27512/07_2025/8dlr_27512.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlr_27512/07_2025/8dlr_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_27512/07_2025/8dlr_27512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlr_27512/07_2025/8dlr_27512.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlr_27512/07_2025/8dlr_27512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlr_27512/07_2025/8dlr_27512.cif" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.10, per 1000 atoms: 1.02 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: 0.99 Conformation dependent library (CDL) restraints added in 486.9 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: 0.59 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: 1.19 Time building geometry restraints manager: 1.19 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: 180.470 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.620 Find NCS groups from input model: 0.030 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:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 208.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP H 66 HIS 0.002 0.001 HIS A 245 PHE 0.030 0.003 PHE H 48 TYR 0.017 0.002 TYR H 79 ARG 0.013 0.001 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 6) link_NAG-ASN : angle 3.35917 ( 18) hydrogen bonds : bond 0.13212 ( 150) hydrogen bonds : angle 6.94746 ( 405) SS BOND : bond 0.00469 ( 5) SS BOND : angle 1.85266 ( 10) covalent geometry : bond 0.00625 ( 4125) covalent geometry : angle 0.81081 ( 5609) *********************** 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 : 0.430 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: 1.2576 time to fit residues: 108.6538 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 : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.0770 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.101621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.075451 restraints weight = 6231.197| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.52 r_work: 0.2878 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4136 Z= 0.153 Angle : 0.562 6.530 5637 Z= 0.293 Chirality : 0.045 0.236 641 Planarity : 0.005 0.049 705 Dihedral : 6.553 56.258 670 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.37), residues: 495 helix: -1.40 (1.23), residues: 17 sheet: -0.13 (0.34), residues: 210 loop : -0.37 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 134 HIS 0.001 0.000 HIS A 245 PHE 0.013 0.001 PHE A 133 TYR 0.010 0.001 TYR L 105 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 6) link_NAG-ASN : angle 2.44291 ( 18) hydrogen bonds : bond 0.02909 ( 150) hydrogen bonds : angle 5.68828 ( 405) SS BOND : bond 0.00613 ( 5) SS BOND : angle 1.14921 ( 10) covalent geometry : bond 0.00345 ( 4125) covalent geometry : angle 0.54367 ( 5609) *********************** 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 77 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.499 Fit side-chains REVERT: A 154 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8652 (mt-10) REVERT: H 82 LYS cc_start: 0.9049 (tmtt) cc_final: 0.8751 (tmtm) REVERT: H 86 ARG cc_start: 0.8297 (mtp180) cc_final: 0.7919 (ttp-170) REVERT: L 88 ASN cc_start: 0.8137 (m-40) cc_final: 0.7791 (m110) REVERT: L 102 GLU cc_start: 0.8734 (tt0) cc_final: 0.8335 (tt0) outliers start: 4 outliers final: 3 residues processed: 76 average time/residue: 1.3512 time to fit residues: 106.4899 Evaluate side-chains 64 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.098839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.071286 restraints weight = 6015.115| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.62 r_work: 0.2756 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4136 Z= 0.231 Angle : 0.590 5.632 5637 Z= 0.306 Chirality : 0.046 0.244 641 Planarity : 0.004 0.044 705 Dihedral : 6.479 51.543 670 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.37), residues: 495 helix: -0.98 (1.35), residues: 17 sheet: -0.03 (0.36), residues: 195 loop : -0.38 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.002 0.001 HIS A 146 PHE 0.021 0.002 PHE A 175 TYR 0.012 0.001 TYR L 105 ARG 0.001 0.000 ARG L 80 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 6) link_NAG-ASN : angle 2.49801 ( 18) hydrogen bonds : bond 0.03223 ( 150) hydrogen bonds : angle 5.63848 ( 405) SS BOND : bond 0.00353 ( 5) SS BOND : angle 1.34183 ( 10) covalent geometry : bond 0.00528 ( 4125) covalent geometry : angle 0.57113 ( 5609) *********************** 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 : 0.483 Fit side-chains REVERT: A 52 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8181 (tp40) REVERT: H 82 LYS cc_start: 0.9008 (tmtt) cc_final: 0.8676 (tmtm) REVERT: H 86 ARG cc_start: 0.8382 (mtp180) cc_final: 0.8065 (ttp-170) REVERT: L 23 GLU cc_start: 0.8350 (pp20) cc_final: 0.8111 (pp20) REVERT: L 88 ASN cc_start: 0.8281 (m-40) cc_final: 0.7901 (m110) REVERT: L 102 GLU cc_start: 0.8766 (tt0) cc_final: 0.8382 (tt0) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 1.4177 time to fit residues: 101.0323 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 : 0.503 ------------------------------------------------------------------------------- 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 19 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 29 optimal weight: 0.0000 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 ** L 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.100591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.074376 restraints weight = 6263.937| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.52 r_work: 0.2857 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1538 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= 0.167 Angle : 0.567 7.505 5637 Z= 0.295 Chirality : 0.044 0.230 641 Planarity : 0.004 0.041 705 Dihedral : 6.246 49.101 670 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.38 % Allowed : 11.01 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.37), residues: 495 helix: -0.77 (1.38), residues: 17 sheet: -0.07 (0.36), residues: 194 loop : -0.31 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.001 0.000 HIS A 245 PHE 0.014 0.001 PHE A 175 TYR 0.009 0.001 TYR A 269 ARG 0.001 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 6) link_NAG-ASN : angle 2.43290 ( 18) hydrogen bonds : bond 0.02825 ( 150) hydrogen bonds : angle 5.45683 ( 405) SS BOND : bond 0.00357 ( 5) SS BOND : angle 2.42482 ( 10) covalent geometry : bond 0.00388 ( 4125) covalent geometry : angle 0.54219 ( 5609) *********************** 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 72 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.441 Fit side-chains REVERT: A 52 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8138 (tp40) REVERT: H 82 LYS cc_start: 0.8991 (tmtt) cc_final: 0.8752 (tmtm) REVERT: H 86 ARG cc_start: 0.8403 (mtp180) cc_final: 0.8079 (ttm170) REVERT: L 88 ASN cc_start: 0.8197 (m-40) cc_final: 0.7878 (m110) REVERT: L 102 GLU cc_start: 0.8707 (tt0) cc_final: 0.8253 (tt0) outliers start: 6 outliers final: 2 residues processed: 70 average time/residue: 1.2776 time to fit residues: 92.4092 Evaluate side-chains 66 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN 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 9 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.098811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.071524 restraints weight = 6145.408| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.59 r_work: 0.2755 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4136 Z= 0.184 Angle : 0.576 7.324 5637 Z= 0.298 Chirality : 0.044 0.234 641 Planarity : 0.004 0.040 705 Dihedral : 6.061 49.479 670 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.06 % Allowed : 11.93 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.37), residues: 495 helix: -0.69 (1.38), residues: 17 sheet: -0.01 (0.36), residues: 194 loop : -0.29 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.001 0.000 HIS A 146 PHE 0.016 0.001 PHE A 175 TYR 0.010 0.001 TYR A 269 ARG 0.001 0.000 ARG A 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 6) link_NAG-ASN : angle 2.42460 ( 18) hydrogen bonds : bond 0.02860 ( 150) hydrogen bonds : angle 5.41476 ( 405) SS BOND : bond 0.00380 ( 5) SS BOND : angle 2.38304 ( 10) covalent geometry : bond 0.00426 ( 4125) covalent geometry : angle 0.55209 ( 5609) *********************** 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 72 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.590 Fit side-chains REVERT: A 52 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8136 (tp40) REVERT: H 57 ARG cc_start: 0.8929 (ptt180) cc_final: 0.8713 (ptm160) REVERT: H 82 LYS cc_start: 0.8958 (tmtt) cc_final: 0.8614 (tmtm) REVERT: H 86 ARG cc_start: 0.8411 (mtp180) cc_final: 0.8004 (ttm170) REVERT: L 88 ASN cc_start: 0.8071 (m-40) cc_final: 0.7624 (m110) REVERT: L 102 GLU cc_start: 0.8704 (tt0) cc_final: 0.8220 (tt0) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 1.8016 time to fit residues: 127.0301 Evaluate side-chains 68 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.099512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.071826 restraints weight = 5984.076| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.64 r_work: 0.2765 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4136 Z= 0.160 Angle : 0.565 7.770 5637 Z= 0.294 Chirality : 0.044 0.229 641 Planarity : 0.004 0.039 705 Dihedral : 5.813 49.341 670 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.37), residues: 495 helix: -0.62 (1.37), residues: 17 sheet: -0.01 (0.36), residues: 194 loop : -0.29 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.001 0.000 HIS A 245 PHE 0.013 0.001 PHE A 175 TYR 0.010 0.001 TYR H 114 ARG 0.001 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 6) link_NAG-ASN : angle 2.39841 ( 18) hydrogen bonds : bond 0.02717 ( 150) hydrogen bonds : angle 5.31865 ( 405) SS BOND : bond 0.00421 ( 5) SS BOND : angle 2.24776 ( 10) covalent geometry : bond 0.00371 ( 4125) covalent geometry : angle 0.54178 ( 5609) *********************** 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 : 0.495 Fit side-chains REVERT: A 52 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8152 (tp40) REVERT: A 154 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8455 (mt-10) REVERT: H 67 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8081 (mtp) REVERT: H 82 LYS cc_start: 0.8976 (tmtt) cc_final: 0.8752 (tmtm) REVERT: H 86 ARG cc_start: 0.8429 (mtp180) cc_final: 0.8061 (ttm170) REVERT: H 127 LYS cc_start: 0.9111 (pttm) cc_final: 0.8850 (pttt) REVERT: L 88 ASN cc_start: 0.8104 (m-40) cc_final: 0.7679 (m110) REVERT: L 102 GLU cc_start: 0.8708 (tt0) cc_final: 0.8219 (mt-10) REVERT: L 122 LYS cc_start: 0.8431 (ttpp) cc_final: 0.8166 (tttt) outliers start: 9 outliers final: 5 residues processed: 70 average time/residue: 2.5888 time to fit residues: 186.9702 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 : 0.862 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3372 r_free = 0.3372 target = 0.100502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.072753 restraints weight = 6056.429| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.66 r_work: 0.2782 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4136 Z= 0.137 Angle : 0.552 8.613 5637 Z= 0.287 Chirality : 0.044 0.224 641 Planarity : 0.004 0.039 705 Dihedral : 5.622 49.420 670 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.29 % Allowed : 12.16 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.37), residues: 495 helix: -0.56 (1.38), residues: 17 sheet: 0.06 (0.35), residues: 202 loop : -0.18 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.001 0.000 HIS A 245 PHE 0.011 0.001 PHE A 175 TYR 0.009 0.001 TYR H 114 ARG 0.001 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 6) link_NAG-ASN : angle 2.38378 ( 18) hydrogen bonds : bond 0.02562 ( 150) hydrogen bonds : angle 5.20752 ( 405) SS BOND : bond 0.00380 ( 5) SS BOND : angle 1.96766 ( 10) covalent geometry : bond 0.00317 ( 4125) covalent geometry : angle 0.53012 ( 5609) *********************** 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 71 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.505 Fit side-chains REVERT: A 52 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8147 (tp40) REVERT: A 154 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8500 (mt-10) REVERT: H 67 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8019 (mtp) REVERT: H 82 LYS cc_start: 0.9004 (tmtt) cc_final: 0.8692 (tmtm) REVERT: H 86 ARG cc_start: 0.8426 (mtp180) cc_final: 0.8058 (ttm170) REVERT: H 106 ARG cc_start: 0.8365 (mtt180) cc_final: 0.7879 (mtm-85) REVERT: H 127 LYS cc_start: 0.9112 (pttm) cc_final: 0.8860 (pttt) REVERT: L 88 ASN cc_start: 0.8141 (m-40) cc_final: 0.7652 (m110) REVERT: L 102 GLU cc_start: 0.8646 (tt0) cc_final: 0.8147 (mt-10) REVERT: L 122 LYS cc_start: 0.8388 (ttpp) cc_final: 0.8133 (tttt) outliers start: 10 outliers final: 4 residues processed: 67 average time/residue: 1.3390 time to fit residues: 92.9037 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.099022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.071674 restraints weight = 5958.867| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.61 r_work: 0.2758 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1843 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= 0.194 Angle : 0.595 9.642 5637 Z= 0.308 Chirality : 0.045 0.236 641 Planarity : 0.004 0.039 705 Dihedral : 5.740 49.669 670 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.61 % Allowed : 13.53 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.37), residues: 495 helix: -0.50 (1.40), residues: 17 sheet: -0.04 (0.35), residues: 205 loop : -0.32 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.001 0.000 HIS A 146 PHE 0.016 0.001 PHE A 175 TYR 0.011 0.001 TYR A 269 ARG 0.001 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 6) link_NAG-ASN : angle 2.44625 ( 18) hydrogen bonds : bond 0.02858 ( 150) hydrogen bonds : angle 5.28742 ( 405) SS BOND : bond 0.00472 ( 5) SS BOND : angle 2.16824 ( 10) covalent geometry : bond 0.00447 ( 4125) covalent geometry : angle 0.57262 ( 5609) *********************** 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 68 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.469 Fit side-chains REVERT: A 52 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8160 (tp40) REVERT: A 154 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8588 (mt-10) REVERT: H 38 LYS cc_start: 0.8978 (tptm) cc_final: 0.8702 (tptm) REVERT: H 76 ILE cc_start: 0.8495 (pt) cc_final: 0.8251 (pp) REVERT: H 82 LYS cc_start: 0.8983 (tmtt) cc_final: 0.8655 (tmtm) REVERT: H 86 ARG cc_start: 0.8488 (mtp180) cc_final: 0.8103 (ttm170) REVERT: H 106 ARG cc_start: 0.8384 (mtt180) cc_final: 0.7880 (mtm-85) REVERT: L 88 ASN cc_start: 0.8164 (m-40) cc_final: 0.7708 (m110) REVERT: L 102 GLU cc_start: 0.8674 (tt0) cc_final: 0.8173 (mt-10) REVERT: L 122 LYS cc_start: 0.8404 (ttpp) cc_final: 0.8137 (tttt) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 1.3856 time to fit residues: 90.0609 Evaluate side-chains 64 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 0.0050 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.072641 restraints weight = 6027.963| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.66 r_work: 0.2778 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4136 Z= 0.140 Angle : 0.552 8.830 5637 Z= 0.288 Chirality : 0.044 0.228 641 Planarity : 0.004 0.039 705 Dihedral : 5.577 49.377 670 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.15 % Allowed : 14.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.37), residues: 495 helix: -0.50 (1.38), residues: 17 sheet: 0.00 (0.33), residues: 213 loop : -0.21 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.001 0.000 HIS A 49 PHE 0.012 0.001 PHE A 175 TYR 0.009 0.001 TYR H 114 ARG 0.001 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 6) link_NAG-ASN : angle 2.40929 ( 18) hydrogen bonds : bond 0.02598 ( 150) hydrogen bonds : angle 5.14350 ( 405) SS BOND : bond 0.00443 ( 5) SS BOND : angle 1.72274 ( 10) covalent geometry : bond 0.00326 ( 4125) covalent geometry : angle 0.53114 ( 5609) *********************** 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 67 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.706 Fit side-chains REVERT: A 52 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8155 (tp40) REVERT: A 154 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8519 (mt-10) REVERT: H 38 LYS cc_start: 0.8990 (tptm) cc_final: 0.8723 (tptm) REVERT: H 67 MET cc_start: 0.8616 (mtp) cc_final: 0.8356 (mtp) REVERT: H 86 ARG cc_start: 0.8486 (mtp180) cc_final: 0.8077 (ttm170) REVERT: H 100 MET cc_start: 0.9094 (tmm) cc_final: 0.8878 (tmt) REVERT: H 106 ARG cc_start: 0.8399 (mtt180) cc_final: 0.7885 (mtm-85) REVERT: H 127 LYS cc_start: 0.9106 (pttm) cc_final: 0.8851 (pttt) REVERT: L 88 ASN cc_start: 0.8164 (m-40) cc_final: 0.7704 (m110) REVERT: L 102 GLU cc_start: 0.8673 (tt0) cc_final: 0.8177 (mt-10) REVERT: L 122 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8143 (tttt) outliers start: 5 outliers final: 4 residues processed: 64 average time/residue: 1.5443 time to fit residues: 102.3234 Evaluate side-chains 65 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.0670 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.101050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.073388 restraints weight = 6047.644| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.66 r_work: 0.2797 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2032 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= 0.117 Angle : 0.534 7.958 5637 Z= 0.279 Chirality : 0.043 0.224 641 Planarity : 0.004 0.039 705 Dihedral : 5.435 49.608 670 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.92 % Allowed : 14.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.38), residues: 495 helix: -0.38 (1.39), residues: 17 sheet: 0.02 (0.33), residues: 213 loop : -0.19 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.001 0.000 HIS A 245 PHE 0.009 0.001 PHE A 238 TYR 0.009 0.001 TYR L 105 ARG 0.002 0.000 ARG H 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 6) link_NAG-ASN : angle 2.32734 ( 18) hydrogen bonds : bond 0.02430 ( 150) hydrogen bonds : angle 5.02372 ( 405) SS BOND : bond 0.00397 ( 5) SS BOND : angle 1.43882 ( 10) covalent geometry : bond 0.00275 ( 4125) covalent geometry : angle 0.51526 ( 5609) ********************** 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 68 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.554 Fit side-chains REVERT: A 154 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8460 (mt-10) REVERT: H 38 LYS cc_start: 0.8959 (tptm) cc_final: 0.8703 (tptm) REVERT: H 67 MET cc_start: 0.8559 (mtp) cc_final: 0.8177 (mtp) REVERT: H 76 ILE cc_start: 0.8560 (pt) cc_final: 0.8324 (pp) REVERT: H 86 ARG cc_start: 0.8486 (mtp180) cc_final: 0.8074 (ttm170) REVERT: H 106 ARG cc_start: 0.8414 (mtt180) cc_final: 0.7879 (mtm-85) REVERT: H 127 LYS cc_start: 0.9087 (pttm) cc_final: 0.8835 (pttt) REVERT: L 88 ASN cc_start: 0.8168 (m-40) cc_final: 0.7730 (m110) REVERT: L 102 GLU cc_start: 0.8599 (tt0) cc_final: 0.8149 (mt-10) REVERT: L 122 LYS cc_start: 0.8363 (ttpp) cc_final: 0.8091 (tttt) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 1.4555 time to fit residues: 98.9854 Evaluate side-chains 65 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 38 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 25 GLN L 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.071107 restraints weight = 6033.676| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.60 r_work: 0.2753 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4136 Z= 0.214 Angle : 0.586 8.533 5637 Z= 0.306 Chirality : 0.045 0.241 641 Planarity : 0.004 0.039 705 Dihedral : 5.726 49.632 670 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.92 % Allowed : 14.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.37), residues: 495 helix: -0.44 (1.39), residues: 17 sheet: 0.01 (0.35), residues: 205 loop : -0.30 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 66 HIS 0.001 0.001 HIS A 146 PHE 0.018 0.002 PHE A 175 TYR 0.011 0.001 TYR H 114 ARG 0.002 0.000 ARG H 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 6) link_NAG-ASN : angle 2.37798 ( 18) hydrogen bonds : bond 0.02924 ( 150) hydrogen bonds : angle 5.18281 ( 405) SS BOND : bond 0.00458 ( 5) SS BOND : angle 1.85500 ( 10) covalent geometry : bond 0.00498 ( 4125) covalent geometry : angle 0.56679 ( 5609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4694.36 seconds wall clock time: 85 minutes 19.75 seconds (5119.75 seconds total)