Starting phenix.real_space_refine on Wed Sep 17 05:55:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lyd_63522/09_2025/9lyd_63522_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lyd_63522/09_2025/9lyd_63522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lyd_63522/09_2025/9lyd_63522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lyd_63522/09_2025/9lyd_63522.map" model { file = "/net/cci-nas-00/data/ceres_data/9lyd_63522/09_2025/9lyd_63522_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lyd_63522/09_2025/9lyd_63522_neut.cif" } resolution = 3.66 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= 0.002 sd= 0.028 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 44 5.16 5 C 3696 2.51 5 N 896 2.21 5 O 1000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5636 Number of models: 1 Model: "" Number of chains: 2 Chain: "Q" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2818 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 357} Chain breaks: 2 Chain: "R" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2818 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 357} Chain breaks: 2 Time building chain proxies: 1.51, per 1000 atoms: 0.27 Number of scatterers: 5636 At special positions: 0 Unit cell: (77.76, 79.68, 103.68, 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 44 16.00 O 1000 8.00 N 896 7.00 C 3696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS Q 177 " - pdb=" SG CYS Q 184 " distance=2.03 Simple disulfide: pdb=" SG CYS R 177 " - pdb=" SG CYS R 184 " 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 TRANS " MET Q1001 " - " ALA Q 224 " " MET R1001 " - " ALA R 224 " Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 234.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 2 sheets defined 76.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'Q' and resid 41 through 68 removed outlier: 3.900A pdb=" N VAL Q 45 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU Q 60 " --> pdb=" O CYS Q 56 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL Q 61 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR Q 68 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 100 removed outlier: 3.584A pdb=" N LEU Q 77 " --> pdb=" O ALA Q 73 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU Q 78 " --> pdb=" O PRO Q 74 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL Q 79 " --> pdb=" O MET Q 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 144 removed outlier: 3.599A pdb=" N LEU Q 110 " --> pdb=" O ALA Q 106 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA Q 141 " --> pdb=" O SER Q 137 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR Q 143 " --> pdb=" O TYR Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 162 removed outlier: 3.553A pdb=" N MET Q 156 " --> pdb=" O ARG Q 152 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU Q 159 " --> pdb=" O VAL Q 155 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TRP Q 161 " --> pdb=" O LEU Q 157 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 174 removed outlier: 4.236A pdb=" N GLY Q 166 " --> pdb=" O GLY Q 162 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU Q 167 " --> pdb=" O GLY Q 163 " (cutoff:3.500A) Proline residue: Q 171 - end of helix removed outlier: 3.640A pdb=" N ALA Q 174 " --> pdb=" O LEU Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 223 removed outlier: 3.698A pdb=" N ARG Q 222 " --> pdb=" O ARG Q 218 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS Q 223 " --> pdb=" O ILE Q 219 " (cutoff:3.500A) Processing helix chain 'Q' and resid 242 through 249 removed outlier: 4.090A pdb=" N LEU Q 249 " --> pdb=" O GLY Q 245 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 270 removed outlier: 3.521A pdb=" N GLY Q 254 " --> pdb=" O ALA Q 250 " (cutoff:3.500A) Proline residue: Q 262 - end of helix Processing helix chain 'Q' and resid 276 through 298 removed outlier: 3.758A pdb=" N TYR Q 280 " --> pdb=" O PRO Q 276 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU Q 284 " --> pdb=" O TYR Q 280 " (cutoff:3.500A) Proline residue: Q 285 - end of helix Proline residue: Q 294 - end of helix Processing helix chain 'Q' and resid 301 through 312 removed outlier: 3.533A pdb=" N GLN Q 305 " --> pdb=" O ASN Q 301 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1002 through 1012 Processing helix chain 'Q' and resid 1022 through 1029 removed outlier: 3.751A pdb=" N GLY Q1029 " --> pdb=" O THR Q1025 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1029 through 1037 removed outlier: 3.514A pdb=" N LYS Q1033 " --> pdb=" O GLY Q1029 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1046 through 1058 Processing helix chain 'Q' and resid 1065 through 1083 Processing helix chain 'Q' and resid 1092 through 1099 removed outlier: 3.737A pdb=" N SER Q1096 " --> pdb=" O CYS Q1092 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL Q1098 " --> pdb=" O GLU Q1094 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1100 through 1104 Processing helix chain 'R' and resid 41 through 68 removed outlier: 3.805A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU R 60 " --> pdb=" O CYS R 56 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL R 61 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR R 68 " --> pdb=" O ILE R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 100 removed outlier: 3.551A pdb=" N LEU R 77 " --> pdb=" O ALA R 73 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU R 78 " --> pdb=" O PRO R 74 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL R 79 " --> pdb=" O MET R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 140 removed outlier: 3.691A pdb=" N ASN R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 168 Processing helix chain 'R' and resid 168 through 173 Processing helix chain 'R' and resid 191 through 221 Processing helix chain 'R' and resid 242 through 260 removed outlier: 4.352A pdb=" N LEU R 253 " --> pdb=" O LEU R 249 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY R 254 " --> pdb=" O ALA R 250 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE R 256 " --> pdb=" O VAL R 252 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS R 259 " --> pdb=" O ALA R 255 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP R 260 " --> pdb=" O PHE R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 267 removed outlier: 3.828A pdb=" N TYR R 266 " --> pdb=" O PRO R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 283 removed outlier: 3.616A pdb=" N TYR R 280 " --> pdb=" O PRO R 276 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 297 removed outlier: 3.738A pdb=" N THR R 287 " --> pdb=" O LEU R 283 " (cutoff:3.500A) Proline residue: R 294 - end of helix removed outlier: 3.530A pdb=" N TYR R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 312 removed outlier: 3.668A pdb=" N GLN R 305 " --> pdb=" O ASN R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 1002 through 1013 Processing helix chain 'R' and resid 1022 through 1029 removed outlier: 4.004A pdb=" N GLY R1029 " --> pdb=" O THR R1025 " (cutoff:3.500A) Processing helix chain 'R' and resid 1029 through 1037 removed outlier: 3.654A pdb=" N LYS R1033 " --> pdb=" O GLY R1029 " (cutoff:3.500A) Processing helix chain 'R' and resid 1046 through 1058 Processing helix chain 'R' and resid 1065 through 1083 Processing helix chain 'R' and resid 1092 through 1099 removed outlier: 3.720A pdb=" N SER R1096 " --> pdb=" O CYS R1092 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL R1098 " --> pdb=" O GLU R1094 " (cutoff:3.500A) Processing helix chain 'R' and resid 1100 through 1104 Processing sheet with id=AA1, first strand: chain 'Q' and resid 1041 through 1043 removed outlier: 8.316A pdb=" N ILE Q1089 " --> pdb=" O LYS Q1016 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY Q1018 " --> pdb=" O ILE Q1089 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE Q1088 " --> pdb=" O ILE Q1109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 1041 through 1043 removed outlier: 8.369A pdb=" N ILE R1089 " --> pdb=" O LYS R1016 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY R1018 " --> pdb=" O ILE R1089 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE R1088 " --> pdb=" O ILE R1109 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1113 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: 0.73 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1382 1.33 - 1.46: 1050 1.46 - 1.58: 3248 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 5744 Sorted by residual: bond pdb=" CB LYS Q 41 " pdb=" CG LYS Q 41 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CB GLU Q1004 " pdb=" CG GLU Q1004 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.85e+00 bond pdb=" CB LYS Q1016 " pdb=" CG LYS Q1016 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CB GLN Q 211 " pdb=" CG GLN Q 211 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" C MET Q1043 " pdb=" N THR Q1044 " ideal model delta sigma weight residual 1.333 1.314 0.019 1.59e-02 3.96e+03 1.37e+00 ... (remaining 5739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 7717 2.90 - 5.81: 85 5.81 - 8.71: 19 8.71 - 11.62: 3 11.62 - 14.52: 2 Bond angle restraints: 7826 Sorted by residual: angle pdb=" N ARG R 222 " pdb=" CA ARG R 222 " pdb=" C ARG R 222 " ideal model delta sigma weight residual 114.56 107.75 6.81 1.27e+00 6.20e-01 2.88e+01 angle pdb=" CA LYS R1075 " pdb=" CB LYS R1075 " pdb=" CG LYS R1075 " ideal model delta sigma weight residual 114.10 124.63 -10.53 2.00e+00 2.50e-01 2.77e+01 angle pdb=" CA LEU R1074 " pdb=" CB LEU R1074 " pdb=" CG LEU R1074 " ideal model delta sigma weight residual 116.30 130.82 -14.52 3.50e+00 8.16e-02 1.72e+01 angle pdb=" CA LYS Q 41 " pdb=" CB LYS Q 41 " pdb=" CG LYS Q 41 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CA LYS Q1016 " pdb=" CB LYS Q1016 " pdb=" CG LYS Q1016 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 ... (remaining 7821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 2943 17.52 - 35.04: 355 35.04 - 52.55: 99 52.55 - 70.07: 11 70.07 - 87.59: 6 Dihedral angle restraints: 3414 sinusoidal: 1266 harmonic: 2148 Sorted by residual: dihedral pdb=" CB CYS R 177 " pdb=" SG CYS R 177 " pdb=" SG CYS R 184 " pdb=" CB CYS R 184 " ideal model delta sinusoidal sigma weight residual -86.00 -26.96 -59.04 1 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" CA LEU R 261 " pdb=" C LEU R 261 " pdb=" N PRO R 262 " pdb=" CA PRO R 262 " ideal model delta harmonic sigma weight residual 180.00 147.62 32.38 0 5.00e+00 4.00e-02 4.19e+01 dihedral pdb=" CG ARG Q 222 " pdb=" CD ARG Q 222 " pdb=" NE ARG Q 222 " pdb=" CZ ARG Q 222 " ideal model delta sinusoidal sigma weight residual -90.00 -40.50 -49.50 2 1.50e+01 4.44e-03 1.23e+01 ... (remaining 3411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 646 0.035 - 0.071: 243 0.071 - 0.106: 67 0.106 - 0.141: 16 0.141 - 0.177: 2 Chirality restraints: 974 Sorted by residual: chirality pdb=" CA LYS R1075 " pdb=" N LYS R1075 " pdb=" C LYS R1075 " pdb=" CB LYS R1075 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CA LEU R1074 " pdb=" N LEU R1074 " pdb=" C LEU R1074 " pdb=" CB LEU R1074 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA LEU Q 53 " pdb=" N LEU Q 53 " pdb=" C LEU Q 53 " pdb=" CB LEU Q 53 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 971 not shown) Planarity restraints: 952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 261 " 0.098 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO R 262 " -0.260 5.00e-02 4.00e+02 pdb=" CA PRO R 262 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO R 262 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR Q 68 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO Q 69 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO Q 69 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO Q 69 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU Q1004 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" CD GLU Q1004 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU Q1004 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU Q1004 " -0.011 2.00e-02 2.50e+03 ... (remaining 949 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 413 2.73 - 3.27: 6119 3.27 - 3.82: 9405 3.82 - 4.36: 9935 4.36 - 4.90: 16899 Nonbonded interactions: 42771 Sorted by model distance: nonbonded pdb=" OE1 GLN Q 215 " pdb=" OH TYR R 135 " model vdw 2.188 3.040 nonbonded pdb=" N GLU Q1032 " pdb=" OE1 GLU Q1032 " model vdw 2.207 3.120 nonbonded pdb=" ND2 ASN R 58 " pdb=" O ALA R 83 " model vdw 2.255 3.120 nonbonded pdb=" N GLU R1047 " pdb=" OE1 GLU R1047 " model vdw 2.256 3.120 nonbonded pdb=" OD1 ASP R 86 " pdb=" OG SER R 290 " model vdw 2.272 3.040 ... (remaining 42766 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: 0.01 Found NCS groups: ncs_group { reference = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 6.720 Find NCS groups from input model: 0.070 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5748 Z= 0.170 Angle : 0.814 14.520 7836 Z= 0.414 Chirality : 0.040 0.177 974 Planarity : 0.007 0.151 950 Dihedral : 16.595 87.590 2026 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.17 % Allowed : 33.33 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.33), residues: 734 helix: 1.60 (0.24), residues: 505 sheet: -0.11 (0.79), residues: 39 loop : -1.03 (0.50), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 222 TYR 0.027 0.002 TYR Q 139 PHE 0.022 0.001 PHE R 256 TRP 0.018 0.001 TRP R 309 HIS 0.011 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 5744) covalent geometry : angle 0.81462 ( 7826) SS BOND : bond 0.00100 ( 2) SS BOND : angle 0.63509 ( 4) hydrogen bonds : bond 0.12228 ( 375) hydrogen bonds : angle 4.73962 ( 1113) link_TRANS : bond 0.00356 ( 2) link_TRANS : angle 0.65674 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.0758 time to fit residues: 17.3068 Evaluate side-chains 176 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 1071 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 211 GLN Q 215 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 293 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 = 0.4000 r_free = 0.4000 target = 0.147280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115357 restraints weight = 10127.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.119121 restraints weight = 5827.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.121617 restraints weight = 4034.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.123196 restraints weight = 3164.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.124233 restraints weight = 2706.277| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5748 Z= 0.145 Angle : 0.670 11.308 7836 Z= 0.335 Chirality : 0.039 0.124 974 Planarity : 0.006 0.115 950 Dihedral : 4.511 48.489 795 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.00 % Favored : 96.87 % Rotamer: Outliers : 4.79 % Allowed : 25.08 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.33), residues: 734 helix: 1.64 (0.24), residues: 519 sheet: -0.05 (0.80), residues: 39 loop : -1.31 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 222 TYR 0.013 0.001 TYR R1058 PHE 0.009 0.001 PHE Q1035 TRP 0.008 0.001 TRP R 309 HIS 0.005 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5744) covalent geometry : angle 0.67018 ( 7826) SS BOND : bond 0.00120 ( 2) SS BOND : angle 0.75308 ( 4) hydrogen bonds : bond 0.05607 ( 375) hydrogen bonds : angle 3.83947 ( 1113) link_TRANS : bond 0.00108 ( 2) link_TRANS : angle 0.59681 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 134 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7902 (tmm-80) REVERT: Q 135 TYR cc_start: 0.8370 (t80) cc_final: 0.7845 (t80) REVERT: Q 140 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7368 (t0) REVERT: Q 268 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8414 (mp) REVERT: Q 1003 GLU cc_start: 0.5953 (tp30) cc_final: 0.5736 (tp30) REVERT: R 1042 ILE cc_start: 0.6851 (mm) cc_final: 0.6632 (mm) REVERT: R 1043 MET cc_start: 0.7248 (tpp) cc_final: 0.6390 (tmm) outliers start: 29 outliers final: 17 residues processed: 192 average time/residue: 0.0831 time to fit residues: 20.3852 Evaluate side-chains 195 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 133 ASP Chi-restraints excluded: chain Q residue 134 ARG Chi-restraints excluded: chain Q residue 140 ASN Chi-restraints excluded: chain Q residue 184 CYS Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain Q residue 221 CYS Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 268 LEU Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain Q residue 1033 LYS Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 MET Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.144562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.112844 restraints weight = 10126.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.116609 restraints weight = 5860.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.119084 restraints weight = 4054.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120651 restraints weight = 3177.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121582 restraints weight = 2712.524| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5748 Z= 0.186 Angle : 0.675 8.997 7836 Z= 0.343 Chirality : 0.040 0.132 974 Planarity : 0.005 0.084 950 Dihedral : 4.135 29.184 792 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.54 % Favored : 96.32 % Rotamer: Outliers : 5.94 % Allowed : 26.24 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.32), residues: 734 helix: 1.58 (0.23), residues: 519 sheet: 0.07 (0.79), residues: 38 loop : -1.30 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R1070 TYR 0.022 0.001 TYR Q 139 PHE 0.010 0.001 PHE Q 256 TRP 0.011 0.001 TRP R 309 HIS 0.002 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 5744) covalent geometry : angle 0.67456 ( 7826) SS BOND : bond 0.00094 ( 2) SS BOND : angle 0.77789 ( 4) hydrogen bonds : bond 0.06166 ( 375) hydrogen bonds : angle 3.86321 ( 1113) link_TRANS : bond 0.00158 ( 2) link_TRANS : angle 0.64853 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 134 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7984 (tmm-80) REVERT: Q 135 TYR cc_start: 0.8443 (t80) cc_final: 0.7917 (t80) REVERT: Q 140 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7423 (t0) REVERT: Q 1003 GLU cc_start: 0.6111 (tp30) cc_final: 0.5872 (tp30) REVERT: R 205 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7494 (m) REVERT: R 252 VAL cc_start: 0.8849 (p) cc_final: 0.8640 (m) REVERT: R 1071 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8003 (mm-30) outliers start: 36 outliers final: 24 residues processed: 191 average time/residue: 0.0777 time to fit residues: 19.2014 Evaluate side-chains 201 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 133 ASP Chi-restraints excluded: chain Q residue 134 ARG Chi-restraints excluded: chain Q residue 137 SER Chi-restraints excluded: chain Q residue 140 ASN Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 184 CYS Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain Q residue 221 CYS Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 284 LEU Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain Q residue 292 ILE Chi-restraints excluded: chain Q residue 1007 LYS Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 MET Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 1001 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 223 HIS ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.145202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113248 restraints weight = 10120.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116950 restraints weight = 5878.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.119422 restraints weight = 4096.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121022 restraints weight = 3219.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.122011 restraints weight = 2749.763| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5748 Z= 0.151 Angle : 0.664 8.250 7836 Z= 0.333 Chirality : 0.039 0.133 974 Planarity : 0.005 0.066 950 Dihedral : 4.077 29.230 792 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.81 % Favored : 96.05 % Rotamer: Outliers : 4.95 % Allowed : 27.89 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.32), residues: 734 helix: 1.66 (0.23), residues: 520 sheet: 0.33 (0.80), residues: 38 loop : -1.29 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 222 TYR 0.021 0.001 TYR Q 139 PHE 0.009 0.001 PHE Q 97 TRP 0.012 0.001 TRP R 309 HIS 0.001 0.000 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5744) covalent geometry : angle 0.66400 ( 7826) SS BOND : bond 0.00232 ( 2) SS BOND : angle 0.93171 ( 4) hydrogen bonds : bond 0.05733 ( 375) hydrogen bonds : angle 3.73430 ( 1113) link_TRANS : bond 0.00089 ( 2) link_TRANS : angle 0.45291 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 111 VAL cc_start: 0.7991 (m) cc_final: 0.7652 (p) REVERT: Q 134 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7699 (tmm-80) REVERT: Q 135 TYR cc_start: 0.8415 (t80) cc_final: 0.7887 (t80) REVERT: Q 211 GLN cc_start: 0.8538 (tp40) cc_final: 0.7995 (tm-30) REVERT: Q 1003 GLU cc_start: 0.6208 (tp30) cc_final: 0.5908 (tp30) REVERT: R 252 VAL cc_start: 0.8837 (p) cc_final: 0.8597 (m) REVERT: R 1071 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8144 (mm-30) outliers start: 30 outliers final: 20 residues processed: 188 average time/residue: 0.0791 time to fit residues: 18.9698 Evaluate side-chains 194 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 133 ASP Chi-restraints excluded: chain Q residue 134 ARG Chi-restraints excluded: chain Q residue 137 SER Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 184 CYS Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain Q residue 292 ILE Chi-restraints excluded: chain Q residue 1007 LYS Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 MET Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.144640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.112723 restraints weight = 10216.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.116475 restraints weight = 5875.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.118934 restraints weight = 4074.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120490 restraints weight = 3196.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121506 restraints weight = 2730.819| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5748 Z= 0.162 Angle : 0.665 8.094 7836 Z= 0.336 Chirality : 0.039 0.131 974 Planarity : 0.005 0.049 950 Dihedral : 4.062 27.423 792 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 5.61 % Allowed : 28.38 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.32), residues: 734 helix: 1.69 (0.23), residues: 518 sheet: 0.43 (0.83), residues: 38 loop : -1.33 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 222 TYR 0.024 0.001 TYR Q 139 PHE 0.025 0.001 PHE R 97 TRP 0.013 0.001 TRP R 309 HIS 0.003 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5744) covalent geometry : angle 0.66525 ( 7826) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.78416 ( 4) hydrogen bonds : bond 0.05853 ( 375) hydrogen bonds : angle 3.75280 ( 1113) link_TRANS : bond 0.00094 ( 2) link_TRANS : angle 0.49142 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 111 VAL cc_start: 0.8065 (m) cc_final: 0.7730 (p) REVERT: Q 134 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7987 (tmm-80) REVERT: Q 211 GLN cc_start: 0.8530 (tp40) cc_final: 0.7936 (tm-30) REVERT: Q 1003 GLU cc_start: 0.6275 (tp30) cc_final: 0.5961 (tp30) REVERT: Q 1071 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: R 204 MET cc_start: 0.7687 (mtt) cc_final: 0.7286 (mtt) REVERT: R 205 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7807 (p) REVERT: R 252 VAL cc_start: 0.8828 (p) cc_final: 0.8572 (m) REVERT: R 1071 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8139 (mm-30) outliers start: 34 outliers final: 25 residues processed: 192 average time/residue: 0.0708 time to fit residues: 17.5840 Evaluate side-chains 201 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 133 ASP Chi-restraints excluded: chain Q residue 134 ARG Chi-restraints excluded: chain Q residue 137 SER Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 184 CYS Chi-restraints excluded: chain Q residue 191 SER Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 284 LEU Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain Q residue 292 ILE Chi-restraints excluded: chain Q residue 1007 LYS Chi-restraints excluded: chain Q residue 1071 GLU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 MET Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 1097 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 13 optimal weight: 0.0030 chunk 15 optimal weight: 0.0060 chunk 64 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.0370 chunk 47 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 overall best weight: 0.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1050 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.149246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117705 restraints weight = 10081.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.121597 restraints weight = 5740.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.124070 restraints weight = 3951.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.125653 restraints weight = 3089.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.126713 restraints weight = 2634.411| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5748 Z= 0.134 Angle : 0.668 8.181 7836 Z= 0.335 Chirality : 0.039 0.134 974 Planarity : 0.005 0.045 950 Dihedral : 3.971 28.270 792 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 4.62 % Allowed : 30.36 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.33), residues: 734 helix: 1.84 (0.24), residues: 518 sheet: 1.32 (0.91), residues: 32 loop : -1.28 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 222 TYR 0.024 0.001 TYR Q 139 PHE 0.017 0.001 PHE R 97 TRP 0.018 0.001 TRP R 309 HIS 0.001 0.000 HIS Q 194 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5744) covalent geometry : angle 0.66839 ( 7826) SS BOND : bond 0.00233 ( 2) SS BOND : angle 0.71874 ( 4) hydrogen bonds : bond 0.04666 ( 375) hydrogen bonds : angle 3.52595 ( 1113) link_TRANS : bond 0.00066 ( 2) link_TRANS : angle 0.40535 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: Q 103 ILE cc_start: 0.8360 (mm) cc_final: 0.8030 (mm) REVERT: Q 135 TYR cc_start: 0.8273 (t80) cc_final: 0.8047 (t80) REVERT: Q 154 TYR cc_start: 0.8084 (m-80) cc_final: 0.7777 (m-80) REVERT: Q 159 LEU cc_start: 0.8365 (tp) cc_final: 0.7939 (tt) REVERT: Q 211 GLN cc_start: 0.8406 (tp40) cc_final: 0.8011 (tm-30) REVERT: Q 1071 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: R 204 MET cc_start: 0.7627 (mtt) cc_final: 0.7192 (mtt) REVERT: R 219 ILE cc_start: 0.8202 (tt) cc_final: 0.7939 (tp) REVERT: R 252 VAL cc_start: 0.8829 (p) cc_final: 0.8559 (m) REVERT: R 1043 MET cc_start: 0.7202 (tpp) cc_final: 0.6432 (tmm) REVERT: R 1071 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8150 (mm-30) outliers start: 28 outliers final: 17 residues processed: 193 average time/residue: 0.0775 time to fit residues: 19.1328 Evaluate side-chains 185 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain Q residue 184 CYS Chi-restraints excluded: chain Q residue 219 ILE Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain Q residue 292 ILE Chi-restraints excluded: chain Q residue 1007 LYS Chi-restraints excluded: chain Q residue 1071 GLU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 MET Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 1097 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.146089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.114203 restraints weight = 10229.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118078 restraints weight = 5844.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.120525 restraints weight = 4026.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.122131 restraints weight = 3161.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.123079 restraints weight = 2701.158| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5748 Z= 0.146 Angle : 0.691 9.215 7836 Z= 0.342 Chirality : 0.039 0.126 974 Planarity : 0.005 0.039 950 Dihedral : 3.947 25.073 792 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 4.79 % Allowed : 31.35 % Favored : 63.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.33), residues: 734 helix: 1.87 (0.24), residues: 512 sheet: 1.13 (0.91), residues: 32 loop : -1.45 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 222 TYR 0.025 0.001 TYR Q 139 PHE 0.024 0.001 PHE R 256 TRP 0.011 0.001 TRP R 309 HIS 0.001 0.000 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5744) covalent geometry : angle 0.69098 ( 7826) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.64595 ( 4) hydrogen bonds : bond 0.05136 ( 375) hydrogen bonds : angle 3.57191 ( 1113) link_TRANS : bond 0.00104 ( 2) link_TRANS : angle 0.41455 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 88 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8133 (tt) REVERT: Q 103 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7996 (mm) REVERT: Q 135 TYR cc_start: 0.8304 (t80) cc_final: 0.8018 (t80) REVERT: Q 154 TYR cc_start: 0.8140 (m-80) cc_final: 0.7843 (m-80) REVERT: Q 159 LEU cc_start: 0.8408 (tp) cc_final: 0.8015 (tt) REVERT: Q 211 GLN cc_start: 0.8383 (tp40) cc_final: 0.7857 (tm-30) REVERT: Q 215 GLN cc_start: 0.8129 (tp40) cc_final: 0.7774 (tp40) REVERT: Q 218 ARG cc_start: 0.8047 (ttm170) cc_final: 0.7813 (ttm110) REVERT: Q 1071 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: R 204 MET cc_start: 0.7733 (mtt) cc_final: 0.7339 (mtt) REVERT: R 296 ILE cc_start: 0.8499 (mt) cc_final: 0.8225 (tt) REVERT: R 1010 LYS cc_start: 0.8798 (tppt) cc_final: 0.8547 (tppt) REVERT: R 1071 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8261 (mm-30) outliers start: 29 outliers final: 21 residues processed: 179 average time/residue: 0.0885 time to fit residues: 20.0735 Evaluate side-chains 188 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 103 ILE Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 133 ASP Chi-restraints excluded: chain Q residue 184 CYS Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain Q residue 1007 LYS Chi-restraints excluded: chain Q residue 1033 LYS Chi-restraints excluded: chain Q residue 1071 GLU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 209 MET Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 MET Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 1001 MET Chi-restraints excluded: chain R residue 1097 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.146173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.114538 restraints weight = 10000.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.118343 restraints weight = 5766.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.120785 restraints weight = 3986.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.122387 restraints weight = 3130.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.123443 restraints weight = 2667.109| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5748 Z= 0.148 Angle : 0.699 8.705 7836 Z= 0.348 Chirality : 0.040 0.125 974 Planarity : 0.005 0.046 950 Dihedral : 3.986 27.442 792 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 4.29 % Allowed : 32.01 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.33), residues: 734 helix: 1.79 (0.23), residues: 514 sheet: 0.75 (0.84), residues: 44 loop : -1.67 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 222 TYR 0.025 0.001 TYR Q 139 PHE 0.019 0.001 PHE R 256 TRP 0.014 0.001 TRP R 309 HIS 0.001 0.000 HIS Q 96 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5744) covalent geometry : angle 0.69874 ( 7826) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.58842 ( 4) hydrogen bonds : bond 0.05271 ( 375) hydrogen bonds : angle 3.57484 ( 1113) link_TRANS : bond 0.00077 ( 2) link_TRANS : angle 0.40062 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: Q 88 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8133 (tt) REVERT: Q 103 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8013 (mm) REVERT: Q 135 TYR cc_start: 0.8311 (t80) cc_final: 0.7969 (t80) REVERT: Q 154 TYR cc_start: 0.8125 (m-80) cc_final: 0.7809 (m-80) REVERT: Q 159 LEU cc_start: 0.8406 (tp) cc_final: 0.8056 (tt) REVERT: Q 211 GLN cc_start: 0.8373 (tp40) cc_final: 0.7938 (tm-30) REVERT: Q 218 ARG cc_start: 0.8037 (ttm170) cc_final: 0.7820 (ttm110) REVERT: Q 1071 GLU cc_start: 0.7992 (tt0) cc_final: 0.7453 (tm-30) REVERT: R 204 MET cc_start: 0.7741 (mtt) cc_final: 0.7337 (mtt) REVERT: R 296 ILE cc_start: 0.8503 (mt) cc_final: 0.8232 (tt) outliers start: 26 outliers final: 21 residues processed: 182 average time/residue: 0.0861 time to fit residues: 19.8746 Evaluate side-chains 191 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 103 ILE Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 133 ASP Chi-restraints excluded: chain Q residue 184 CYS Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain Q residue 292 ILE Chi-restraints excluded: chain Q residue 1007 LYS Chi-restraints excluded: chain Q residue 1033 LYS Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 MET Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.145109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.113210 restraints weight = 10025.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116969 restraints weight = 5791.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.119398 restraints weight = 4038.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121001 restraints weight = 3172.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.121944 restraints weight = 2707.553| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5748 Z= 0.173 Angle : 0.752 9.275 7836 Z= 0.377 Chirality : 0.041 0.145 974 Planarity : 0.005 0.042 950 Dihedral : 4.024 25.281 792 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 4.79 % Allowed : 32.51 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.33), residues: 734 helix: 1.77 (0.23), residues: 514 sheet: 0.55 (0.85), residues: 44 loop : -1.68 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 222 TYR 0.026 0.001 TYR Q 139 PHE 0.020 0.002 PHE Q 97 TRP 0.014 0.001 TRP R 309 HIS 0.002 0.000 HIS Q 96 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5744) covalent geometry : angle 0.75180 ( 7826) SS BOND : bond 0.00164 ( 2) SS BOND : angle 0.68426 ( 4) hydrogen bonds : bond 0.05649 ( 375) hydrogen bonds : angle 3.69982 ( 1113) link_TRANS : bond 0.00116 ( 2) link_TRANS : angle 0.46602 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: Q 88 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8132 (tt) REVERT: Q 103 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7992 (mm) REVERT: Q 135 TYR cc_start: 0.8318 (t80) cc_final: 0.7979 (t80) REVERT: Q 159 LEU cc_start: 0.8372 (tp) cc_final: 0.8041 (tt) REVERT: Q 211 GLN cc_start: 0.8428 (tp40) cc_final: 0.7973 (tm-30) REVERT: Q 1071 GLU cc_start: 0.8018 (tt0) cc_final: 0.7472 (tm-30) REVERT: R 204 MET cc_start: 0.7763 (mtt) cc_final: 0.7367 (mtt) REVERT: R 1010 LYS cc_start: 0.8644 (tppt) cc_final: 0.8281 (tppt) outliers start: 29 outliers final: 22 residues processed: 182 average time/residue: 0.0864 time to fit residues: 20.0197 Evaluate side-chains 190 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain Q residue 103 ILE Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 133 ASP Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 184 CYS Chi-restraints excluded: chain Q residue 209 MET Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain Q residue 1007 LYS Chi-restraints excluded: chain Q residue 1033 LYS Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 209 MET Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 MET Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.145780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.113946 restraints weight = 10181.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.117762 restraints weight = 5858.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.120186 restraints weight = 4063.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.121824 restraints weight = 3189.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.122758 restraints weight = 2712.411| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5748 Z= 0.160 Angle : 0.777 11.011 7836 Z= 0.385 Chirality : 0.041 0.173 974 Planarity : 0.005 0.048 950 Dihedral : 4.070 27.086 792 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 3.47 % Allowed : 34.32 % Favored : 62.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.33), residues: 734 helix: 1.76 (0.23), residues: 514 sheet: 0.54 (0.86), residues: 44 loop : -1.64 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 222 TYR 0.026 0.001 TYR Q 139 PHE 0.019 0.001 PHE Q 97 TRP 0.015 0.001 TRP R 309 HIS 0.001 0.000 HIS Q 194 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 5744) covalent geometry : angle 0.77770 ( 7826) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.62061 ( 4) hydrogen bonds : bond 0.05518 ( 375) hydrogen bonds : angle 3.68445 ( 1113) link_TRANS : bond 0.00062 ( 2) link_TRANS : angle 0.43275 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: Q 103 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7984 (mm) REVERT: Q 135 TYR cc_start: 0.8320 (t80) cc_final: 0.7991 (t80) REVERT: Q 159 LEU cc_start: 0.8361 (tp) cc_final: 0.8040 (tt) REVERT: Q 211 GLN cc_start: 0.8412 (tp40) cc_final: 0.7963 (tm-30) REVERT: Q 1071 GLU cc_start: 0.8011 (tt0) cc_final: 0.7461 (tm-30) REVERT: R 204 MET cc_start: 0.7738 (mtt) cc_final: 0.7350 (mtt) REVERT: R 1010 LYS cc_start: 0.8794 (tppt) cc_final: 0.8498 (tppt) outliers start: 21 outliers final: 18 residues processed: 180 average time/residue: 0.0824 time to fit residues: 18.7919 Evaluate side-chains 188 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 103 ILE Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 184 CYS Chi-restraints excluded: chain Q residue 209 MET Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 269 LEU Chi-restraints excluded: chain Q residue 290 SER Chi-restraints excluded: chain Q residue 292 ILE Chi-restraints excluded: chain Q residue 1007 LYS Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 209 MET Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 MET Chi-restraints excluded: chain R residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 43 optimal weight: 0.0470 chunk 51 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.147904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115852 restraints weight = 10005.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.119688 restraints weight = 5770.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.122115 restraints weight = 4004.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.123737 restraints weight = 3157.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.124640 restraints weight = 2696.169| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5748 Z= 0.148 Angle : 0.773 10.188 7836 Z= 0.382 Chirality : 0.041 0.153 974 Planarity : 0.005 0.040 950 Dihedral : 3.992 24.713 792 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.63 % Favored : 95.23 % Rotamer: Outliers : 3.63 % Allowed : 33.83 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.33), residues: 734 helix: 1.84 (0.23), residues: 512 sheet: 0.25 (0.85), residues: 46 loop : -1.66 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 222 TYR 0.025 0.001 TYR Q 139 PHE 0.037 0.002 PHE R 256 TRP 0.019 0.001 TRP R 309 HIS 0.001 0.000 HIS Q 194 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5744) covalent geometry : angle 0.77293 ( 7826) SS BOND : bond 0.00214 ( 2) SS BOND : angle 0.62321 ( 4) hydrogen bonds : bond 0.04878 ( 375) hydrogen bonds : angle 3.58407 ( 1113) link_TRANS : bond 0.00068 ( 2) link_TRANS : angle 0.38940 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1102.21 seconds wall clock time: 19 minutes 42.81 seconds (1182.81 seconds total)