Starting phenix.real_space_refine on Sun Apr 27 12:21:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lyd_63522/04_2025/9lyd_63522_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lyd_63522/04_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_63522/04_2025/9lyd_63522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lyd_63522/04_2025/9lyd_63522.map" model { file = "/net/cci-nas-00/data/ceres_data/9lyd_63522/04_2025/9lyd_63522_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lyd_63522/04_2025/9lyd_63522_neut.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.08, per 1000 atoms: 0.72 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: 1.42 Conformation dependent library (CDL) restraints added in 937.8 milliseconds 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: 0.53 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: 1.40 Time building geometry restraints manager: 1.68 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: 0.03 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: 0.920 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.900 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.320 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.018 0.001 TRP R 309 HIS 0.011 0.001 HIS Q 223 PHE 0.022 0.001 PHE R 256 TYR 0.027 0.002 TYR Q 139 ARG 0.013 0.001 ARG Q 222 Details of bonding type rmsd link_TRANS : bond 0.00356 ( 2) link_TRANS : angle 0.65674 ( 6) hydrogen bonds : bond 0.12228 ( 375) hydrogen bonds : angle 4.73962 ( 1113) SS BOND : bond 0.00100 ( 2) SS BOND : angle 0.63509 ( 4) covalent geometry : bond 0.00378 ( 5744) covalent geometry : angle 0.81462 ( 7826) *********************** 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 : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.1800 time to fit residues: 41.0398 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 : 0.561 ------------------------------------------------------------------------------- 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 62 optimal weight: 1.9990 chunk 56 optimal weight: 0.0170 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.0270 chunk 35 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.0010 overall best weight: 0.1882 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.149487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117619 restraints weight = 9971.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121397 restraints weight = 5733.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.123939 restraints weight = 3961.541| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5748 Z= 0.134 Angle : 0.666 11.313 7836 Z= 0.331 Chirality : 0.038 0.121 974 Planarity : 0.006 0.115 950 Dihedral : 4.471 46.963 795 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.86 % Favored : 97.00 % Rotamer: Outliers : 4.13 % Allowed : 25.25 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.33), residues: 734 helix: 1.61 (0.24), residues: 525 sheet: -0.00 (0.79), residues: 39 loop : -1.50 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 309 HIS 0.005 0.001 HIS Q 223 PHE 0.011 0.001 PHE R 97 TYR 0.013 0.001 TYR Q 135 ARG 0.005 0.000 ARG Q 222 Details of bonding type rmsd link_TRANS : bond 0.00105 ( 2) link_TRANS : angle 0.55118 ( 6) hydrogen bonds : bond 0.05044 ( 375) hydrogen bonds : angle 3.73879 ( 1113) SS BOND : bond 0.00138 ( 2) SS BOND : angle 0.69157 ( 4) covalent geometry : bond 0.00289 ( 5744) covalent geometry : angle 0.66584 ( 7826) *********************** 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 208 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 47 LEU cc_start: 0.8906 (mt) cc_final: 0.8702 (mm) REVERT: Q 135 TYR cc_start: 0.8381 (t80) cc_final: 0.7890 (t80) REVERT: Q 140 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7352 (t0) REVERT: Q 159 LEU cc_start: 0.8366 (tp) cc_final: 0.7900 (tt) REVERT: Q 1003 GLU cc_start: 0.6018 (tp30) cc_final: 0.5749 (tp30) REVERT: R 299 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6861 (t80) outliers start: 25 outliers final: 13 residues processed: 193 average time/residue: 0.2101 time to fit residues: 51.1923 Evaluate side-chains 190 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 140 ASN 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 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 181 LEU Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 MET Chi-restraints excluded: chain R residue 299 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.146529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.114580 restraints weight = 10168.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118310 restraints weight = 5830.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.120812 restraints weight = 4050.741| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5748 Z= 0.155 Angle : 0.660 8.815 7836 Z= 0.332 Chirality : 0.039 0.134 974 Planarity : 0.005 0.080 950 Dihedral : 4.037 28.430 792 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Rotamer: Outliers : 4.95 % Allowed : 27.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.33), residues: 734 helix: 1.68 (0.24), residues: 519 sheet: 0.19 (0.79), residues: 38 loop : -1.37 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 309 HIS 0.002 0.001 HIS Q 96 PHE 0.008 0.001 PHE Q 97 TYR 0.021 0.001 TYR Q 139 ARG 0.008 0.001 ARG Q 222 Details of bonding type rmsd link_TRANS : bond 0.00130 ( 2) link_TRANS : angle 0.58534 ( 6) hydrogen bonds : bond 0.05501 ( 375) hydrogen bonds : angle 3.69430 ( 1113) SS BOND : bond 0.00094 ( 2) SS BOND : angle 0.64664 ( 4) covalent geometry : bond 0.00345 ( 5744) covalent geometry : angle 0.66024 ( 7826) *********************** 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 205 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 134 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7926 (tmm-80) REVERT: Q 135 TYR cc_start: 0.8387 (t80) cc_final: 0.7903 (t80) REVERT: Q 140 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7420 (t0) REVERT: Q 161 TRP cc_start: 0.8085 (m100) cc_final: 0.7823 (m100) REVERT: Q 1003 GLU cc_start: 0.6007 (tp30) cc_final: 0.5751 (tp30) REVERT: R 66 VAL cc_start: 0.8637 (p) cc_final: 0.8417 (p) REVERT: R 172 VAL cc_start: 0.8214 (p) cc_final: 0.7995 (p) REVERT: R 173 LEU cc_start: 0.8346 (mt) cc_final: 0.8134 (mm) REVERT: R 252 VAL cc_start: 0.8840 (p) cc_final: 0.8630 (m) REVERT: R 1071 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8039 (mm-30) outliers start: 30 outliers final: 20 residues processed: 189 average time/residue: 0.1890 time to fit residues: 45.1564 Evaluate side-chains 195 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 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 1096 SER 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 274 SER 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 34 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.146487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.114743 restraints weight = 10206.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118526 restraints weight = 5846.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.120973 restraints weight = 4031.260| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5748 Z= 0.142 Angle : 0.645 8.352 7836 Z= 0.324 Chirality : 0.039 0.121 974 Planarity : 0.005 0.064 950 Dihedral : 3.993 28.795 792 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.81 % Favored : 96.05 % Rotamer: Outliers : 5.94 % Allowed : 26.73 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.33), residues: 734 helix: 1.72 (0.24), residues: 519 sheet: 0.49 (0.80), residues: 38 loop : -1.41 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 309 HIS 0.001 0.000 HIS R 273 PHE 0.010 0.001 PHE R 97 TYR 0.021 0.001 TYR Q 139 ARG 0.007 0.001 ARG R 222 Details of bonding type rmsd link_TRANS : bond 0.00061 ( 2) link_TRANS : angle 0.40458 ( 6) hydrogen bonds : bond 0.05326 ( 375) hydrogen bonds : angle 3.63959 ( 1113) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.60887 ( 4) covalent geometry : bond 0.00315 ( 5744) covalent geometry : angle 0.64562 ( 7826) *********************** 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: 36 poor density : 168 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 134 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7889 (tmm-80) REVERT: Q 135 TYR cc_start: 0.8376 (t80) cc_final: 0.7869 (t80) REVERT: Q 161 TRP cc_start: 0.8082 (m100) cc_final: 0.7823 (m100) REVERT: Q 211 GLN cc_start: 0.8549 (tp40) cc_final: 0.7982 (tm-30) REVERT: Q 1003 GLU cc_start: 0.6046 (tp30) cc_final: 0.5751 (tp30) REVERT: Q 1010 LYS cc_start: 0.8317 (tppt) cc_final: 0.8098 (tppt) REVERT: R 172 VAL cc_start: 0.8150 (p) cc_final: 0.7911 (p) REVERT: R 173 LEU cc_start: 0.8341 (mt) cc_final: 0.8133 (mm) REVERT: R 205 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7498 (m) REVERT: R 252 VAL cc_start: 0.8840 (p) cc_final: 0.8586 (m) REVERT: R 1043 MET cc_start: 0.7267 (tpp) cc_final: 0.6440 (tmm) REVERT: R 1071 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8181 (mm-30) outliers start: 36 outliers final: 22 residues processed: 188 average time/residue: 0.1820 time to fit residues: 43.0940 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 : 0.527 ------------------------------------------------------------------------------- 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 169 LEU 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 1071 GLU Chi-restraints excluded: chain Q residue 1096 SER 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 274 SER 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 42 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 chunk 71 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.147539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115493 restraints weight = 10096.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.119298 restraints weight = 5827.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.121781 restraints weight = 4038.800| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1491 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= 0.130 Angle : 0.648 8.085 7836 Z= 0.321 Chirality : 0.038 0.118 974 Planarity : 0.004 0.046 950 Dihedral : 3.899 27.328 792 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 5.78 % Allowed : 28.88 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.33), residues: 734 helix: 1.78 (0.24), residues: 519 sheet: 0.58 (0.81), residues: 38 loop : -1.38 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 309 HIS 0.001 0.000 HIS Q 194 PHE 0.012 0.001 PHE R1035 TYR 0.021 0.001 TYR Q 139 ARG 0.008 0.001 ARG Q 222 Details of bonding type rmsd link_TRANS : bond 0.00081 ( 2) link_TRANS : angle 0.47073 ( 6) hydrogen bonds : bond 0.05013 ( 375) hydrogen bonds : angle 3.55617 ( 1113) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.78575 ( 4) covalent geometry : bond 0.00288 ( 5744) covalent geometry : angle 0.64801 ( 7826) *********************** 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 212 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 103 ILE cc_start: 0.8344 (mm) cc_final: 0.8007 (mm) REVERT: Q 134 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7870 (tmm-80) REVERT: Q 161 TRP cc_start: 0.8074 (m100) cc_final: 0.7812 (m100) REVERT: Q 211 GLN cc_start: 0.8516 (tp40) cc_final: 0.7985 (tm-30) REVERT: Q 1003 GLU cc_start: 0.6150 (tp30) cc_final: 0.5829 (tp30) REVERT: Q 1008 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8333 (tmmt) REVERT: R 173 LEU cc_start: 0.8328 (mt) cc_final: 0.8103 (mm) REVERT: R 205 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7511 (m) REVERT: R 219 ILE cc_start: 0.8268 (tt) cc_final: 0.8029 (tp) REVERT: R 252 VAL cc_start: 0.8845 (p) cc_final: 0.8585 (m) REVERT: R 1071 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8236 (mm-30) outliers start: 35 outliers final: 22 residues processed: 194 average time/residue: 0.1896 time to fit residues: 46.5450 Evaluate side-chains 194 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 131 THR Chi-restraints excluded: chain Q residue 133 ASP Chi-restraints excluded: chain Q residue 134 ARG 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 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 Q residue 1096 SER Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 274 SER 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 53 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.145380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113365 restraints weight = 10027.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.117020 restraints weight = 5841.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.119499 restraints weight = 4084.162| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5748 Z= 0.167 Angle : 0.679 8.941 7836 Z= 0.340 Chirality : 0.040 0.137 974 Planarity : 0.004 0.048 950 Dihedral : 3.989 27.428 792 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Rotamer: Outliers : 5.45 % Allowed : 29.70 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.32), residues: 734 helix: 1.74 (0.23), residues: 514 sheet: 0.43 (0.83), residues: 38 loop : -1.49 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 309 HIS 0.002 0.001 HIS Q 96 PHE 0.009 0.001 PHE R 97 TYR 0.025 0.001 TYR Q 139 ARG 0.010 0.001 ARG Q 222 Details of bonding type rmsd link_TRANS : bond 0.00116 ( 2) link_TRANS : angle 0.54583 ( 6) hydrogen bonds : bond 0.05668 ( 375) hydrogen bonds : angle 3.64823 ( 1113) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.74118 ( 4) covalent geometry : bond 0.00370 ( 5744) covalent geometry : angle 0.67938 ( 7826) *********************** 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 206 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 134 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7964 (tmm-80) REVERT: Q 154 TYR cc_start: 0.8151 (m-80) cc_final: 0.7863 (m-80) REVERT: Q 161 TRP cc_start: 0.8105 (m100) cc_final: 0.7855 (m100) REVERT: Q 211 GLN cc_start: 0.8521 (tp40) cc_final: 0.7992 (tm-30) REVERT: Q 1003 GLU cc_start: 0.6157 (tp30) cc_final: 0.5873 (tp30) REVERT: Q 1008 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8327 (tmmt) REVERT: R 172 VAL cc_start: 0.8167 (p) cc_final: 0.7961 (p) REVERT: R 173 LEU cc_start: 0.8374 (mt) cc_final: 0.8166 (mm) REVERT: R 204 MET cc_start: 0.7634 (mtt) cc_final: 0.7251 (mtt) REVERT: R 205 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7886 (p) REVERT: R 252 VAL cc_start: 0.8841 (p) cc_final: 0.8575 (m) REVERT: R 1043 MET cc_start: 0.7331 (tpp) cc_final: 0.6404 (tmm) REVERT: R 1071 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8200 (mm-30) outliers start: 33 outliers final: 24 residues processed: 186 average time/residue: 0.1925 time to fit residues: 45.0911 Evaluate side-chains 198 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 82 LEU 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 169 LEU Chi-restraints excluded: chain Q residue 184 CYS Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain Q residue 265 VAL 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 Q residue 1096 SER Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 157 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 274 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.145612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.113637 restraints weight = 10061.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.117375 restraints weight = 5825.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.119803 restraints weight = 4061.025| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5748 Z= 0.149 Angle : 0.674 8.800 7836 Z= 0.337 Chirality : 0.039 0.130 974 Planarity : 0.004 0.045 950 Dihedral : 3.921 26.786 792 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 4.62 % Allowed : 31.35 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.32), residues: 734 helix: 1.81 (0.23), residues: 514 sheet: 0.50 (0.85), residues: 38 loop : -1.50 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 309 HIS 0.001 0.000 HIS R 96 PHE 0.012 0.001 PHE R 97 TYR 0.026 0.001 TYR Q 139 ARG 0.010 0.001 ARG Q 222 Details of bonding type rmsd link_TRANS : bond 0.00092 ( 2) link_TRANS : angle 0.49795 ( 6) hydrogen bonds : bond 0.05468 ( 375) hydrogen bonds : angle 3.59973 ( 1113) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.67994 ( 4) covalent geometry : bond 0.00333 ( 5744) covalent geometry : angle 0.67432 ( 7826) *********************** 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 203 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 134 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7897 (tmm-80) REVERT: Q 135 TYR cc_start: 0.8409 (t80) cc_final: 0.7879 (t80) REVERT: Q 154 TYR cc_start: 0.8151 (m-80) cc_final: 0.7824 (m-80) REVERT: Q 161 TRP cc_start: 0.8099 (m100) cc_final: 0.7828 (m100) REVERT: Q 211 GLN cc_start: 0.8479 (tp40) cc_final: 0.7945 (tm-30) REVERT: Q 1008 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8303 (tmmt) REVERT: R 172 VAL cc_start: 0.8150 (p) cc_final: 0.7856 (p) REVERT: R 173 LEU cc_start: 0.8358 (mt) cc_final: 0.8047 (mm) REVERT: R 204 MET cc_start: 0.7646 (mtt) cc_final: 0.7273 (mtt) REVERT: R 205 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7885 (p) REVERT: R 252 VAL cc_start: 0.8834 (p) cc_final: 0.8564 (m) REVERT: R 1043 MET cc_start: 0.7369 (tpp) cc_final: 0.6497 (tmm) REVERT: R 1071 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8262 (mm-30) outliers start: 28 outliers final: 21 residues processed: 188 average time/residue: 0.1871 time to fit residues: 44.2740 Evaluate side-chains 195 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 169 LEU 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 1096 SER 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 205 VAL Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 274 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 21 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.145849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.114037 restraints weight = 10005.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.117831 restraints weight = 5781.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120258 restraints weight = 4006.763| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5748 Z= 0.141 Angle : 0.673 8.487 7836 Z= 0.337 Chirality : 0.039 0.125 974 Planarity : 0.004 0.045 950 Dihedral : 3.881 26.920 792 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 4.79 % Allowed : 31.02 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.33), residues: 734 helix: 1.86 (0.23), residues: 514 sheet: 1.18 (0.84), residues: 42 loop : -1.68 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 309 HIS 0.001 0.000 HIS Q 194 PHE 0.012 0.001 PHE R 97 TYR 0.024 0.001 TYR Q 139 ARG 0.010 0.000 ARG Q 222 Details of bonding type rmsd link_TRANS : bond 0.00070 ( 2) link_TRANS : angle 0.47609 ( 6) hydrogen bonds : bond 0.05262 ( 375) hydrogen bonds : angle 3.56873 ( 1113) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.64125 ( 4) covalent geometry : bond 0.00317 ( 5744) covalent geometry : angle 0.67334 ( 7826) *********************** 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 198 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: Q 88 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8147 (tt) REVERT: Q 103 ILE cc_start: 0.8346 (mm) cc_final: 0.8026 (mm) REVERT: Q 134 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7911 (tmm-80) REVERT: Q 154 TYR cc_start: 0.8133 (m-80) cc_final: 0.7812 (m-80) REVERT: Q 159 LEU cc_start: 0.8400 (tp) cc_final: 0.7977 (tt) REVERT: Q 161 TRP cc_start: 0.8119 (m100) cc_final: 0.7850 (m100) REVERT: Q 211 GLN cc_start: 0.8446 (tp40) cc_final: 0.7916 (tm-30) REVERT: R 204 MET cc_start: 0.7640 (mtt) cc_final: 0.7275 (mtt) REVERT: R 205 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7518 (m) REVERT: R 211 GLN cc_start: 0.8453 (tp40) cc_final: 0.8217 (tp40) REVERT: R 252 VAL cc_start: 0.8841 (p) cc_final: 0.8563 (m) REVERT: R 1071 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8296 (mm-30) outliers start: 29 outliers final: 22 residues processed: 184 average time/residue: 0.1938 time to fit residues: 44.9333 Evaluate side-chains 193 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU 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 169 LEU 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 Q residue 1096 SER 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 205 VAL Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 274 SER Chi-restraints excluded: chain R residue 290 SER Chi-restraints excluded: chain R residue 291 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.145277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.113333 restraints weight = 10102.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.117055 restraints weight = 5864.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119575 restraints weight = 4076.164| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5748 Z= 0.156 Angle : 0.720 9.061 7836 Z= 0.360 Chirality : 0.040 0.127 974 Planarity : 0.004 0.041 950 Dihedral : 3.890 26.142 792 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 5.28 % Allowed : 31.19 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.32), residues: 734 helix: 1.85 (0.23), residues: 512 sheet: 0.82 (0.85), residues: 44 loop : -1.73 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 309 HIS 0.001 0.000 HIS R 96 PHE 0.024 0.001 PHE Q 97 TYR 0.027 0.001 TYR Q 139 ARG 0.010 0.001 ARG Q 222 Details of bonding type rmsd link_TRANS : bond 0.00071 ( 2) link_TRANS : angle 0.45321 ( 6) hydrogen bonds : bond 0.05419 ( 375) hydrogen bonds : angle 3.59885 ( 1113) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.66699 ( 4) covalent geometry : bond 0.00354 ( 5744) covalent geometry : angle 0.72043 ( 7826) *********************** 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 200 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: Q 88 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8143 (tt) REVERT: Q 134 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7915 (tmm-80) REVERT: Q 154 TYR cc_start: 0.8133 (m-80) cc_final: 0.7775 (m-80) REVERT: Q 159 LEU cc_start: 0.8414 (tp) cc_final: 0.7998 (tt) REVERT: Q 211 GLN cc_start: 0.8461 (tp40) cc_final: 0.7899 (tm-30) REVERT: Q 1010 LYS cc_start: 0.8064 (tppt) cc_final: 0.7862 (mttp) REVERT: R 204 MET cc_start: 0.7664 (mtt) cc_final: 0.7308 (mtt) REVERT: R 205 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7535 (m) REVERT: R 211 GLN cc_start: 0.8439 (tp40) cc_final: 0.8219 (tp40) REVERT: R 252 VAL cc_start: 0.8837 (p) cc_final: 0.8559 (m) outliers start: 32 outliers final: 21 residues processed: 184 average time/residue: 0.1889 time to fit residues: 43.8790 Evaluate side-chains 192 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU 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 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 1096 SER Chi-restraints excluded: chain R residue 84 VAL 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 274 SER 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 25 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 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 = 0.3996 r_free = 0.3996 target = 0.145818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.113784 restraints weight = 10058.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117558 restraints weight = 5817.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120060 restraints weight = 4048.561| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5748 Z= 0.155 Angle : 0.760 9.619 7836 Z= 0.379 Chirality : 0.041 0.159 974 Planarity : 0.005 0.044 950 Dihedral : 3.985 26.745 792 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 4.62 % Allowed : 31.85 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.32), residues: 734 helix: 1.83 (0.23), residues: 512 sheet: 0.33 (0.94), residues: 34 loop : -1.47 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 309 HIS 0.001 0.000 HIS Q 194 PHE 0.019 0.001 PHE Q 97 TYR 0.026 0.001 TYR Q 139 ARG 0.010 0.001 ARG Q 222 Details of bonding type rmsd link_TRANS : bond 0.00055 ( 2) link_TRANS : angle 0.45029 ( 6) hydrogen bonds : bond 0.05437 ( 375) hydrogen bonds : angle 3.64333 ( 1113) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.64705 ( 4) covalent geometry : bond 0.00353 ( 5744) covalent geometry : angle 0.76027 ( 7826) ********************** 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 199 residues out of total 606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: Q 88 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8192 (tt) REVERT: Q 134 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7922 (tmm-80) REVERT: Q 159 LEU cc_start: 0.8404 (tp) cc_final: 0.7997 (tt) REVERT: Q 211 GLN cc_start: 0.8452 (tp40) cc_final: 0.7921 (tm-30) REVERT: R 205 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7522 (m) REVERT: R 211 GLN cc_start: 0.8441 (tp40) cc_final: 0.8227 (tp40) REVERT: R 252 VAL cc_start: 0.8833 (p) cc_final: 0.8552 (m) REVERT: R 1010 LYS cc_start: 0.7985 (tppt) cc_final: 0.7743 (mttp) outliers start: 28 outliers final: 23 residues processed: 184 average time/residue: 0.1936 time to fit residues: 44.7527 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 : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU 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 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 1096 SER 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 205 VAL Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 274 SER 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 2 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.0570 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.147201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114963 restraints weight = 10078.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.118798 restraints weight = 5809.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.121297 restraints weight = 4026.313| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2209 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= 0.148 Angle : 0.759 10.209 7836 Z= 0.375 Chirality : 0.040 0.147 974 Planarity : 0.005 0.040 950 Dihedral : 3.944 25.639 792 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 4.46 % Allowed : 32.51 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.33), residues: 734 helix: 1.88 (0.23), residues: 511 sheet: 0.16 (0.84), residues: 46 loop : -1.74 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 309 HIS 0.001 0.000 HIS Q 194 PHE 0.021 0.001 PHE Q 97 TYR 0.026 0.001 TYR Q 139 ARG 0.010 0.001 ARG Q 222 Details of bonding type rmsd link_TRANS : bond 0.00044 ( 2) link_TRANS : angle 0.42810 ( 6) hydrogen bonds : bond 0.05085 ( 375) hydrogen bonds : angle 3.58825 ( 1113) SS BOND : bond 0.00177 ( 2) SS BOND : angle 0.61720 ( 4) covalent geometry : bond 0.00333 ( 5744) covalent geometry : angle 0.75930 ( 7826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.10 seconds wall clock time: 39 minutes 58.65 seconds (2398.65 seconds total)