Starting phenix.real_space_refine on Thu Jul 2 04:29:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qzq_53474/07_2026/9qzq_53474.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qzq_53474/07_2026/9qzq_53474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qzq_53474/07_2026/9qzq_53474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qzq_53474/07_2026/9qzq_53474.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qzq_53474/07_2026/9qzq_53474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qzq_53474/07_2026/9qzq_53474.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 40 5.16 5 Na 2 4.78 5 C 4165 2.51 5 N 1061 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6479 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2188 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 16, 'TRANS': 269} Chain breaks: 1 Chain: "H" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1722 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 216} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1582 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 197} Chain: "N" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 985 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' NA': 2} Chain breaks: 2 Time building chain proxies: 1.64, per 1000 atoms: 0.25 Number of scatterers: 6479 At special positions: 0 Unit cell: (106.92, 106.92, 125.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 Na 2 11.00 O 1211 8.00 N 1061 7.00 C 4165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 93 " 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 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 413.5 milliseconds 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1554 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 13 sheets defined 32.7% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 21 through 39 removed outlier: 3.696A pdb=" N LEU A 27 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE A 37 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 70 removed outlier: 3.583A pdb=" N ALA A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 83 removed outlier: 3.631A pdb=" N GLY A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.914A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.525A pdb=" N VAL A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix removed outlier: 4.092A pdb=" N ARG A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 166 Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.614A pdb=" N CYS A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 211 removed outlier: 3.688A pdb=" N MET A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 185 " --> pdb=" O PRO A 181 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.823A pdb=" N MET A 215 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.767A pdb=" N MET A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.608A pdb=" N LEU A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 102C removed outlier: 3.555A pdb=" N HIS H 102B" --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 194 removed outlier: 3.992A pdb=" N GLN H 194 " --> pdb=" O LEU H 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 4.025A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 189 removed outlier: 3.778A pdb=" N HIS L 189 " --> pdb=" O TYR L 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 88 removed outlier: 3.647A pdb=" N THR N 88 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.653A pdb=" N SER H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR H 90 " --> pdb=" O THR H 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 122 through 126 removed outlier: 3.523A pdb=" N LEU H 126 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY H 141 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR H 178 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 122 through 126 removed outlier: 3.523A pdb=" N LEU H 126 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY H 141 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR H 178 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 153 through 156 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.523A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.731A pdb=" N SER L 114 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER L 176 " --> pdb=" O SER L 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.625A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.566A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.585A pdb=" N ALA N 96 " --> pdb=" O THR N 33 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG N 38 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLY N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR N 59 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 327 hydrogen bonds defined for protein. 885 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: 0.92 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2004 1.34 - 1.46: 1634 1.46 - 1.58: 2933 1.58 - 1.70: 0 1.70 - 1.81: 59 Bond restraints: 6630 Sorted by residual: bond pdb=" C ILE A 168 " pdb=" N PRO A 169 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.36e-02 5.41e+03 3.26e+00 bond pdb=" C ILE A 71 " pdb=" O ILE A 71 " ideal model delta sigma weight residual 1.233 1.244 -0.011 1.02e-02 9.61e+03 1.16e+00 bond pdb=" SD MET A 34 " pdb=" CE MET A 34 " ideal model delta sigma weight residual 1.791 1.765 0.026 2.50e-02 1.60e+03 1.07e+00 bond pdb=" CA MET A 34 " pdb=" C MET A 34 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.24e-02 6.50e+03 9.42e-01 bond pdb=" C GLN L 38 " pdb=" N LYS L 39 " ideal model delta sigma weight residual 1.329 1.311 0.018 1.86e-02 2.89e+03 9.41e-01 ... (remaining 6625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 8544 1.26 - 2.52: 382 2.52 - 3.78: 58 3.78 - 5.04: 13 5.04 - 6.30: 6 Bond angle restraints: 9003 Sorted by residual: angle pdb=" N VAL L 133 " pdb=" CA VAL L 133 " pdb=" C VAL L 133 " ideal model delta sigma weight residual 108.35 113.91 -5.56 1.32e+00 5.74e-01 1.77e+01 angle pdb=" N VAL N 64 " pdb=" CA VAL N 64 " pdb=" C VAL N 64 " ideal model delta sigma weight residual 113.20 109.61 3.59 9.60e-01 1.09e+00 1.40e+01 angle pdb=" C MET A 34 " pdb=" CA MET A 34 " pdb=" CB MET A 34 " ideal model delta sigma weight residual 110.96 106.10 4.86 1.54e+00 4.22e-01 9.95e+00 angle pdb=" C PHE A 33 " pdb=" N MET A 34 " pdb=" CA MET A 34 " ideal model delta sigma weight residual 120.65 124.53 -3.88 1.32e+00 5.74e-01 8.66e+00 angle pdb=" C ALA L 32 " pdb=" N VAL L 33 " pdb=" CA VAL L 33 " ideal model delta sigma weight residual 120.49 123.89 -3.40 1.38e+00 5.25e-01 6.06e+00 ... (remaining 8998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.34: 3273 15.34 - 30.68: 438 30.68 - 46.02: 165 46.02 - 61.36: 40 61.36 - 76.70: 10 Dihedral angle restraints: 3926 sinusoidal: 1484 harmonic: 2442 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual 93.00 52.51 40.49 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CG ARG L 108 " pdb=" CD ARG L 108 " pdb=" NE ARG L 108 " pdb=" CZ ARG L 108 " ideal model delta sinusoidal sigma weight residual -90.00 -43.43 -46.57 2 1.50e+01 4.44e-03 1.13e+01 dihedral pdb=" CA ASP N 55 " pdb=" CB ASP N 55 " pdb=" CG ASP N 55 " pdb=" OD1 ASP N 55 " ideal model delta sinusoidal sigma weight residual -30.00 -85.40 55.40 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 3923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 797 0.044 - 0.087: 167 0.087 - 0.131: 59 0.131 - 0.174: 2 0.174 - 0.218: 1 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CB VAL A 166 " pdb=" CA VAL A 166 " pdb=" CG1 VAL A 166 " pdb=" CG2 VAL A 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ILE H 197 " pdb=" N ILE H 197 " pdb=" C ILE H 197 " pdb=" CB ILE H 197 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA VAL H 152 " pdb=" N VAL H 152 " pdb=" C VAL H 152 " pdb=" CB VAL H 152 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1023 not shown) Planarity restraints: 1124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 285 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO A 286 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO L 59 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO A 220 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.018 5.00e-02 4.00e+02 ... (remaining 1121 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 616 2.75 - 3.29: 6188 3.29 - 3.83: 10669 3.83 - 4.36: 12492 4.36 - 4.90: 22290 Nonbonded interactions: 52255 Sorted by model distance: nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR H 133 " pdb=" O THR H 137 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR H 50 " pdb=" OE1 GLN H 102 " model vdw 2.216 3.040 nonbonded pdb=" NH2 ARG A 21 " pdb=" OD1 ASN A 209 " model vdw 2.218 3.120 nonbonded pdb=" O PRO L 8 " pdb=" OG1 THR L 102 " model vdw 2.230 3.040 ... (remaining 52250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.610 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: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.470 Find NCS groups from input model: 0.030 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 : 0.003 0.029 6634 Z= 0.141 Angle : 0.621 6.303 9011 Z= 0.386 Chirality : 0.041 0.218 1026 Planarity : 0.004 0.052 1124 Dihedral : 16.464 76.703 2360 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.28 % Allowed : 26.25 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.29), residues: 839 helix: 0.10 (0.34), residues: 239 sheet: -0.51 (0.37), residues: 222 loop : -1.00 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 108 TYR 0.009 0.001 TYR N 50 PHE 0.012 0.001 PHE A 310 TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 ( 6630) covalent geometry : angle 0.62062 / 0.39 ( 9003) SS BOND : bond 0.00281 / 0.14 ( 4) SS BOND : angle 0.53818 / 0.32 ( 8) hydrogen bonds : bond 0.21818 / 14.12 ( 304) hydrogen bonds : angle 8.84983 / 6.43 ( 885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.392 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 83 average time/residue: 0.0913 time to fit residues: 10.0233 Evaluate side-chains 82 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 135 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.0070 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 0.3980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.192636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.148877 restraints weight = 7224.040| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.25 r_work: 0.3043 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6634 Z= 0.145 Angle : 0.548 7.099 9011 Z= 0.286 Chirality : 0.042 0.143 1026 Planarity : 0.004 0.047 1124 Dihedral : 3.914 55.662 920 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.08 % Allowed : 25.69 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.29), residues: 839 helix: 0.56 (0.34), residues: 240 sheet: -0.48 (0.34), residues: 233 loop : -1.08 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 108 TYR 0.010 0.001 TYR N 50 PHE 0.015 0.001 PHE N 27 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 6630) covalent geometry : angle 0.54798 / 0.29 ( 9003) SS BOND : bond 0.00538 / 0.27 ( 4) SS BOND : angle 0.94691 / 0.56 ( 8) hydrogen bonds : bond 0.04350 / 2.76 ( 304) hydrogen bonds : angle 6.05762 / 4.45 ( 885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.256 Fit side-chains REVERT: L 166 GLN cc_start: 0.6390 (tt0) cc_final: 0.6163 (tt0) outliers start: 15 outliers final: 9 residues processed: 93 average time/residue: 0.0865 time to fit residues: 10.6893 Evaluate side-chains 89 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain N residue 73 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.192906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.148278 restraints weight = 7217.190| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.51 r_work: 0.3119 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6634 Z= 0.133 Angle : 0.515 7.119 9011 Z= 0.265 Chirality : 0.041 0.143 1026 Planarity : 0.004 0.046 1124 Dihedral : 3.430 14.530 917 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.19 % Allowed : 23.61 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.28), residues: 839 helix: 0.70 (0.34), residues: 241 sheet: -0.52 (0.32), residues: 238 loop : -0.97 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 83 TYR 0.008 0.001 TYR N 50 PHE 0.016 0.001 PHE N 27 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 6630) covalent geometry : angle 0.51461 / 0.26 ( 9003) SS BOND : bond 0.00465 / 0.23 ( 4) SS BOND : angle 0.83905 / 0.50 ( 8) hydrogen bonds : bond 0.03482 / 2.23 ( 304) hydrogen bonds : angle 5.42224 / 3.97 ( 885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.276 Fit side-chains REVERT: A 24 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: L 95 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8302 (pp) REVERT: N 6 GLU cc_start: 0.8606 (mp0) cc_final: 0.8339 (mp0) outliers start: 23 outliers final: 14 residues processed: 102 average time/residue: 0.0875 time to fit residues: 11.7912 Evaluate side-chains 94 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain N residue 73 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 12 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 83AASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.192660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.149034 restraints weight = 7215.722| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.47 r_work: 0.3128 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6634 Z= 0.179 Angle : 0.554 7.232 9011 Z= 0.282 Chirality : 0.043 0.254 1026 Planarity : 0.004 0.046 1124 Dihedral : 3.627 15.374 917 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.58 % Allowed : 21.39 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.28), residues: 839 helix: 0.69 (0.33), residues: 241 sheet: -0.49 (0.32), residues: 238 loop : -0.93 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.010 0.001 TYR H 90 PHE 0.021 0.001 PHE N 27 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 6630) covalent geometry : angle 0.55331 / 0.28 ( 9003) SS BOND : bond 0.00517 / 0.26 ( 4) SS BOND : angle 1.00422 / 0.59 ( 8) hydrogen bonds : bond 0.03516 / 2.25 ( 304) hydrogen bonds : angle 5.25576 / 3.86 ( 885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.251 Fit side-chains REVERT: A 24 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7339 (m-30) REVERT: A 176 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5942 (tp) REVERT: A 310 PHE cc_start: 0.5574 (m-80) cc_final: 0.5330 (m-80) REVERT: L 95 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8340 (pp) outliers start: 33 outliers final: 22 residues processed: 105 average time/residue: 0.0835 time to fit residues: 11.7476 Evaluate side-chains 101 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 88 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 0.0030 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 30.0000 chunk 55 optimal weight: 0.0670 overall best weight: 1.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.193258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.149479 restraints weight = 7190.459| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.52 r_work: 0.3111 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6634 Z= 0.157 Angle : 0.536 7.242 9011 Z= 0.272 Chirality : 0.043 0.212 1026 Planarity : 0.004 0.045 1124 Dihedral : 3.614 15.589 917 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.58 % Allowed : 21.11 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.28), residues: 839 helix: 0.78 (0.33), residues: 241 sheet: -0.41 (0.32), residues: 238 loop : -0.87 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.008 0.001 TYR L 49 PHE 0.018 0.001 PHE N 27 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 6630) covalent geometry : angle 0.53553 / 0.27 ( 9003) SS BOND : bond 0.00483 / 0.24 ( 4) SS BOND : angle 0.82628 / 0.49 ( 8) hydrogen bonds : bond 0.03293 / 2.11 ( 304) hydrogen bonds : angle 5.11492 / 3.75 ( 885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.257 Fit side-chains REVERT: A 24 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7350 (m-30) REVERT: A 112 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8007 (ttm) REVERT: A 176 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6171 (tp) REVERT: A 310 PHE cc_start: 0.5683 (m-80) cc_final: 0.5444 (m-80) REVERT: L 95 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8349 (pp) outliers start: 33 outliers final: 25 residues processed: 106 average time/residue: 0.0820 time to fit residues: 11.7809 Evaluate side-chains 106 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 GLN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 88 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 83AASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.192612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.149521 restraints weight = 7243.367| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.35 r_work: 0.3143 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6634 Z= 0.185 Angle : 0.556 7.248 9011 Z= 0.283 Chirality : 0.044 0.181 1026 Planarity : 0.004 0.046 1124 Dihedral : 3.747 19.046 917 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 5.00 % Allowed : 21.81 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.29), residues: 839 helix: 0.76 (0.33), residues: 241 sheet: -0.37 (0.32), residues: 240 loop : -0.87 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.008 0.001 TYR H 90 PHE 0.021 0.001 PHE N 27 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 ( 6630) covalent geometry : angle 0.55518 / 0.28 ( 9003) SS BOND : bond 0.00523 / 0.26 ( 4) SS BOND : angle 0.95296 / 0.56 ( 8) hydrogen bonds : bond 0.03399 / 2.17 ( 304) hydrogen bonds : angle 5.11444 / 3.75 ( 885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.309 Fit side-chains REVERT: A 24 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: A 176 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6156 (tp) REVERT: A 310 PHE cc_start: 0.5728 (m-80) cc_final: 0.5459 (m-80) REVERT: L 95 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8383 (pp) outliers start: 36 outliers final: 27 residues processed: 106 average time/residue: 0.0842 time to fit residues: 11.8813 Evaluate side-chains 106 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 GLN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 142 CYS Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 88 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 33 optimal weight: 0.0030 chunk 44 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.0020 chunk 6 optimal weight: 2.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 166 GLN N 83AASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.196557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151433 restraints weight = 7141.926| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.29 r_work: 0.3242 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6634 Z= 0.103 Angle : 0.497 7.187 9011 Z= 0.255 Chirality : 0.042 0.249 1026 Planarity : 0.004 0.043 1124 Dihedral : 3.536 17.307 917 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.03 % Allowed : 23.06 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.29), residues: 839 helix: 1.13 (0.33), residues: 240 sheet: -0.16 (0.32), residues: 234 loop : -0.85 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.007 0.001 TYR N 50 PHE 0.012 0.001 PHE N 27 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 6630) covalent geometry : angle 0.49744 / 0.26 ( 9003) SS BOND : bond 0.00305 / 0.15 ( 4) SS BOND : angle 0.51956 / 0.31 ( 8) hydrogen bonds : bond 0.02980 / 1.88 ( 304) hydrogen bonds : angle 4.81319 / 3.52 ( 885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.262 Fit side-chains REVERT: L 95 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8331 (pp) outliers start: 29 outliers final: 21 residues processed: 101 average time/residue: 0.0800 time to fit residues: 10.8544 Evaluate side-chains 100 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 142 CYS Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 88 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 83AASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.196281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.159504 restraints weight = 7019.081| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.50 r_work: 0.3181 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6634 Z= 0.124 Angle : 0.510 7.194 9011 Z= 0.261 Chirality : 0.043 0.238 1026 Planarity : 0.004 0.043 1124 Dihedral : 3.543 15.678 917 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.17 % Allowed : 23.33 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.29), residues: 839 helix: 1.19 (0.34), residues: 237 sheet: -0.07 (0.33), residues: 234 loop : -0.77 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.008 0.001 TYR N 92 PHE 0.017 0.001 PHE A 310 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 6630) covalent geometry : angle 0.50975 / 0.26 ( 9003) SS BOND : bond 0.00412 / 0.20 ( 4) SS BOND : angle 0.67700 / 0.40 ( 8) hydrogen bonds : bond 0.03020 / 1.90 ( 304) hydrogen bonds : angle 4.75712 / 3.49 ( 885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.238 Fit side-chains REVERT: A 176 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5936 (tp) REVERT: A 261 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: L 95 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8357 (pp) REVERT: L 197 THR cc_start: 0.5044 (OUTLIER) cc_final: 0.4808 (t) outliers start: 30 outliers final: 23 residues processed: 99 average time/residue: 0.0796 time to fit residues: 10.7163 Evaluate side-chains 101 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 102 GLN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 142 CYS Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 88 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 0.0570 chunk 72 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.201730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.163431 restraints weight = 7061.931| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.63 r_work: 0.3304 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6634 Z= 0.099 Angle : 0.494 7.249 9011 Z= 0.250 Chirality : 0.042 0.233 1026 Planarity : 0.004 0.042 1124 Dihedral : 3.414 13.401 917 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.47 % Allowed : 24.44 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.29), residues: 839 helix: 1.26 (0.34), residues: 245 sheet: 0.04 (0.33), residues: 234 loop : -0.71 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.007 0.001 TYR L 49 PHE 0.012 0.001 PHE N 27 TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 6630) covalent geometry : angle 0.49400 / 0.25 ( 9003) SS BOND : bond 0.00300 / 0.15 ( 4) SS BOND : angle 0.56525 / 0.33 ( 8) hydrogen bonds : bond 0.02803 / 1.76 ( 304) hydrogen bonds : angle 4.56415 / 3.34 ( 885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.244 Fit side-chains REVERT: A 176 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6206 (tp) REVERT: A 261 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: L 95 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8346 (pp) REVERT: L 197 THR cc_start: 0.5196 (OUTLIER) cc_final: 0.4916 (t) outliers start: 25 outliers final: 19 residues processed: 95 average time/residue: 0.0858 time to fit residues: 11.0209 Evaluate side-chains 97 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 142 CYS Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 30.0000 chunk 15 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.197800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.167577 restraints weight = 6876.259| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.25 r_work: 0.3383 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6634 Z= 0.174 Angle : 0.549 7.245 9011 Z= 0.279 Chirality : 0.044 0.240 1026 Planarity : 0.004 0.045 1124 Dihedral : 3.653 16.814 917 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.75 % Allowed : 23.75 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.29), residues: 839 helix: 1.22 (0.34), residues: 237 sheet: -0.11 (0.32), residues: 240 loop : -0.64 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 83 TYR 0.011 0.001 TYR N 59 PHE 0.020 0.001 PHE N 27 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 ( 6630) covalent geometry : angle 0.54859 / 0.28 ( 9003) SS BOND : bond 0.00546 / 0.27 ( 4) SS BOND : angle 0.93989 / 0.56 ( 8) hydrogen bonds : bond 0.03215 / 2.05 ( 304) hydrogen bonds : angle 4.78050 / 3.51 ( 885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.188 Fit side-chains REVERT: A 176 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6118 (tp) REVERT: A 261 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: L 95 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8414 (pp) REVERT: L 197 THR cc_start: 0.5050 (OUTLIER) cc_final: 0.4814 (t) outliers start: 27 outliers final: 21 residues processed: 99 average time/residue: 0.0841 time to fit residues: 11.2602 Evaluate side-chains 101 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 142 CYS Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 79 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 83AASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.200856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.169750 restraints weight = 6896.430| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.21 r_work: 0.3465 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6634 Z= 0.101 Angle : 0.498 7.200 9011 Z= 0.253 Chirality : 0.042 0.227 1026 Planarity : 0.004 0.043 1124 Dihedral : 3.454 13.348 917 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.61 % Allowed : 23.61 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.29), residues: 839 helix: 1.45 (0.34), residues: 236 sheet: 0.09 (0.33), residues: 234 loop : -0.58 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.011 0.001 TYR H 50 PHE 0.012 0.001 PHE N 27 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 6630) covalent geometry : angle 0.49787 / 0.25 ( 9003) SS BOND : bond 0.00300 / 0.15 ( 4) SS BOND : angle 0.55484 / 0.33 ( 8) hydrogen bonds : bond 0.02811 / 1.77 ( 304) hydrogen bonds : angle 4.62084 / 3.39 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2155.29 seconds wall clock time: 37 minutes 38.49 seconds (2258.49 seconds total)