Starting phenix.real_space_refine on Thu Jul 2 03:41:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vu6_63963/07_2026/9vu6_63963.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vu6_63963/07_2026/9vu6_63963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vu6_63963/07_2026/9vu6_63963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vu6_63963/07_2026/9vu6_63963.map" model { file = "/net/cci-nas-00/data/ceres_data/9vu6_63963/07_2026/9vu6_63963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vu6_63963/07_2026/9vu6_63963.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.085 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 P 44 5.49 5 S 24 5.16 5 C 3840 2.51 5 N 1065 2.21 5 O 1275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 6248 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1832 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain breaks: 1 Chain: "B" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2150 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Chain: "C" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "D" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1059 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "E" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 460 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "F" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 442 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 1.47, per 1000 atoms: 0.24 Number of scatterers: 6248 At special positions: 0 Unit cell: (90.4932, 95.8797, 116.348, 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 24 16.00 P 44 15.00 O 1275 8.00 N 1065 7.00 C 3840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.39 Conformation dependent library (CDL) restraints added in 313.5 milliseconds 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1230 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 40.2% alpha, 13.1% beta 21 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 135 through 166 Processing helix chain 'A' and resid 187 through 199 removed outlier: 4.248A pdb=" N LEU A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.598A pdb=" N MET A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.613A pdb=" N LEU A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 243' Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.751A pdb=" N GLY A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 removed outlier: 3.521A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 110 through 116 removed outlier: 4.301A pdb=" N LEU B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 147 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 216 through 220 removed outlier: 4.013A pdb=" N ASP B 219 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Processing helix chain 'B' and resid 288 through 291 Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 162 through 184 Processing helix chain 'D' and resid 13 through 25 removed outlier: 4.263A pdb=" N TYR D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 removed outlier: 4.048A pdb=" N PHE D 42 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 43 " --> pdb=" O HIS D 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 38 through 43' Processing helix chain 'D' and resid 51 through 62 Processing helix chain 'D' and resid 69 through 76 removed outlier: 3.981A pdb=" N ILE D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 96 removed outlier: 3.944A pdb=" N CYS D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.896A pdb=" N TYR D 104 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 127 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 removed outlier: 3.682A pdb=" N ILE A 179 " --> pdb=" O SER A 367 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU A 352 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL A 205 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE A 354 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET A 207 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP A 204 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 274 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 306 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 272 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE A 324 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR A 277 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N SER A 326 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL A 279 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 72 through 73 removed outlier: 6.771A pdb=" N LYS B 72 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N MET B 303 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA B 93 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU B 305 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE B 95 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER B 92 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N PHE B 130 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 94 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N TRP B 132 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE B 96 " --> pdb=" O TRP B 132 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE B 235 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B 236 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN B 155 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N MET B 238 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N PHE B 259 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N MET B 157 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP B 261 " --> pdb=" O MET B 157 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASN B 159 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE B 263 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 161 " --> pdb=" O PHE B 263 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1772 1.34 - 1.46: 1415 1.46 - 1.58: 3142 1.58 - 1.70: 86 1.70 - 1.82: 42 Bond restraints: 6457 Sorted by residual: bond pdb=" C1' DC F 12 " pdb=" N1 DC F 12 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.47e+01 bond pdb=" C3' DC F 20 " pdb=" C2' DC F 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DA E 12 " pdb=" C2' DA E 12 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.42e+00 bond pdb=" C3' DA F 19 " pdb=" C2' DA F 19 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.38e+00 bond pdb=" C3' DA E 14 " pdb=" C2' DA E 14 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.04e+00 ... (remaining 6452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 8785 3.65 - 7.30: 77 7.30 - 10.94: 8 10.94 - 14.59: 0 14.59 - 18.24: 1 Bond angle restraints: 8871 Sorted by residual: angle pdb=" N ASN B 125 " pdb=" CA ASN B 125 " pdb=" C ASN B 125 " ideal model delta sigma weight residual 113.43 106.81 6.62 1.26e+00 6.30e-01 2.76e+01 angle pdb=" CA LEU C 173 " pdb=" CB LEU C 173 " pdb=" CG LEU C 173 " ideal model delta sigma weight residual 116.30 134.54 -18.24 3.50e+00 8.16e-02 2.72e+01 angle pdb=" N ASN D 133 " pdb=" CA ASN D 133 " pdb=" CB ASN D 133 " ideal model delta sigma weight residual 114.17 108.46 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" CA ILE A 276 " pdb=" CB ILE A 276 " pdb=" CG1 ILE A 276 " ideal model delta sigma weight residual 110.40 118.42 -8.02 1.70e+00 3.46e-01 2.23e+01 angle pdb=" N3 DT E 17 " pdb=" C4 DT E 17 " pdb=" O4 DT E 17 " ideal model delta sigma weight residual 119.90 122.72 -2.82 6.00e-01 2.78e+00 2.20e+01 ... (remaining 8866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.47: 3355 30.47 - 60.94: 460 60.94 - 91.42: 41 91.42 - 121.89: 0 121.89 - 152.36: 2 Dihedral angle restraints: 3858 sinusoidal: 1963 harmonic: 1895 Sorted by residual: dihedral pdb=" CA VAL A 366 " pdb=" C VAL A 366 " pdb=" N SER A 367 " pdb=" CA SER A 367 " ideal model delta harmonic sigma weight residual 180.00 -155.95 -24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASP D 13 " pdb=" C ASP D 13 " pdb=" N PHE D 14 " pdb=" CA PHE D 14 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA HIS B 252 " pdb=" C HIS B 252 " pdb=" N GLN B 253 " pdb=" CA GLN B 253 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 627 0.044 - 0.087: 251 0.087 - 0.131: 60 0.131 - 0.174: 11 0.174 - 0.218: 3 Chirality restraints: 952 Sorted by residual: chirality pdb=" CG LEU C 173 " pdb=" CB LEU C 173 " pdb=" CD1 LEU C 173 " pdb=" CD2 LEU C 173 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN D 128 " pdb=" N ASN D 128 " pdb=" C ASN D 128 " pdb=" CB ASN D 128 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" C3' DA F 13 " pdb=" C4' DA F 13 " pdb=" O3' DA F 13 " pdb=" C2' DA F 13 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 949 not shown) Planarity restraints: 986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 70 " -0.017 2.00e-02 2.50e+03 1.72e-02 7.40e+00 pdb=" CG TRP D 70 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 70 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 70 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 70 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 70 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 70 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 70 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 70 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 193 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" CG ASP A 193 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP A 193 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 193 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 13 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" CG ASP D 13 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP D 13 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP D 13 " -0.013 2.00e-02 2.50e+03 ... (remaining 983 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 572 2.74 - 3.28: 6031 3.28 - 3.82: 10659 3.82 - 4.36: 12682 4.36 - 4.90: 20392 Nonbonded interactions: 50336 Sorted by model distance: nonbonded pdb=" OG SER B 110 " pdb=" OE1 GLU B 112 " model vdw 2.203 3.040 nonbonded pdb=" NE2 HIS A 198 " pdb=" OD2 ASP D 24 " model vdw 2.266 3.120 nonbonded pdb=" O CYS A 346 " pdb=" OH TYR A 351 " model vdw 2.271 3.040 nonbonded pdb=" O ASP A 174 " pdb=" NH2 ARG D 22 " model vdw 2.285 3.120 nonbonded pdb=" N THR C 152 " pdb=" OD1 ASP C 155 " model vdw 2.300 3.120 ... (remaining 50331 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.170 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:1.140 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 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 : 0.005 0.080 6457 Z= 0.346 Angle : 0.923 18.238 8871 Z= 0.597 Chirality : 0.050 0.218 952 Planarity : 0.005 0.076 986 Dihedral : 24.310 152.358 2628 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.29 % Favored : 90.55 % Rotamer: Outliers : 3.24 % Allowed : 37.65 % Favored : 59.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.31), residues: 635 helix: -0.99 (0.31), residues: 226 sheet: -1.61 (0.52), residues: 98 loop : -2.02 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 197 TYR 0.020 0.002 TYR D 103 PHE 0.030 0.002 PHE B 130 TRP 0.046 0.002 TRP D 70 HIS 0.002 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.35 ( 6457) covalent geometry : angle 0.92297 / 0.60 ( 8871) hydrogen bonds : bond 0.15331 / 9.64 ( 230) hydrogen bonds : angle 6.56896 / 4.86 ( 620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: B 71 TYR cc_start: 0.7837 (p90) cc_final: 0.7440 (p90) REVERT: B 276 MET cc_start: 0.5133 (OUTLIER) cc_final: 0.3937 (mmt) REVERT: D 56 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8561 (mmtm) REVERT: D 70 TRP cc_start: 0.6355 (m100) cc_final: 0.5801 (m100) REVERT: D 73 ILE cc_start: 0.5499 (OUTLIER) cc_final: 0.4912 (tp) REVERT: D 88 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: D 111 GLU cc_start: 0.8720 (pm20) cc_final: 0.8406 (pm20) REVERT: D 115 GLU cc_start: 0.8658 (tp30) cc_final: 0.8323 (tm-30) outliers start: 19 outliers final: 14 residues processed: 122 average time/residue: 0.0737 time to fit residues: 11.8981 Evaluate side-chains 120 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 88 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 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 = 0.4501 r_free = 0.4501 target = 0.211312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.166282 restraints weight = 7788.366| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.53 r_work: 0.3795 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6457 Z= 0.153 Angle : 0.702 14.679 8871 Z= 0.382 Chirality : 0.046 0.250 952 Planarity : 0.004 0.067 986 Dihedral : 23.821 158.551 1258 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.79 % Allowed : 32.88 % Favored : 61.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.33), residues: 635 helix: -0.39 (0.32), residues: 234 sheet: -1.46 (0.53), residues: 98 loop : -1.90 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 197 TYR 0.011 0.001 TYR B 152 PHE 0.013 0.001 PHE A 250 TRP 0.014 0.001 TRP D 70 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 6457) covalent geometry : angle 0.70232 / 0.38 ( 8871) hydrogen bonds : bond 0.06097 / 3.82 ( 230) hydrogen bonds : angle 5.01219 / 3.65 ( 620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.227 Fit side-chains REVERT: A 257 LYS cc_start: 0.7421 (mmtm) cc_final: 0.7151 (mmmm) REVERT: B 71 TYR cc_start: 0.7938 (p90) cc_final: 0.7429 (p90) REVERT: B 77 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6945 (pmmt) REVERT: C 172 ASN cc_start: 0.8504 (m110) cc_final: 0.8287 (m110) REVERT: C 180 ARG cc_start: 0.7975 (tmm-80) cc_final: 0.7682 (tmm-80) REVERT: D 32 LEU cc_start: 0.7305 (mp) cc_final: 0.6957 (mt) REVERT: D 41 TYR cc_start: 0.7947 (t80) cc_final: 0.7630 (t80) REVERT: D 56 LYS cc_start: 0.9118 (mmmm) cc_final: 0.8857 (mmtm) REVERT: D 73 ILE cc_start: 0.5360 (OUTLIER) cc_final: 0.4883 (tp) REVERT: D 102 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5776 (pm20) REVERT: D 111 GLU cc_start: 0.8669 (pm20) cc_final: 0.8370 (pm20) REVERT: D 112 GLU cc_start: 0.8824 (mp0) cc_final: 0.8011 (mp0) REVERT: D 115 GLU cc_start: 0.8536 (tp30) cc_final: 0.8262 (tm-30) REVERT: D 116 ILE cc_start: 0.7775 (pt) cc_final: 0.7208 (tp) outliers start: 34 outliers final: 14 residues processed: 142 average time/residue: 0.0813 time to fit residues: 15.1186 Evaluate side-chains 125 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 27 optimal weight: 0.0670 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.212236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.164990 restraints weight = 7774.663| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.47 r_work: 0.3786 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6457 Z= 0.155 Angle : 0.664 7.253 8871 Z= 0.370 Chirality : 0.045 0.225 952 Planarity : 0.004 0.065 986 Dihedral : 23.895 158.451 1238 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 6.47 % Allowed : 31.18 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.33), residues: 635 helix: -0.26 (0.33), residues: 234 sheet: -1.53 (0.52), residues: 98 loop : -1.85 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 180 TYR 0.020 0.001 TYR D 103 PHE 0.014 0.001 PHE A 250 TRP 0.016 0.001 TRP D 70 HIS 0.003 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 6457) covalent geometry : angle 0.66442 / 0.37 ( 8871) hydrogen bonds : bond 0.05883 / 3.68 ( 230) hydrogen bonds : angle 4.83621 / 3.53 ( 620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 257 LYS cc_start: 0.7446 (mmtm) cc_final: 0.7181 (mmmm) REVERT: A 275 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6355 (mt-10) REVERT: B 71 TYR cc_start: 0.7998 (p90) cc_final: 0.7484 (p90) REVERT: B 114 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6865 (tt) REVERT: B 153 ILE cc_start: 0.6302 (OUTLIER) cc_final: 0.5952 (pp) REVERT: D 41 TYR cc_start: 0.7951 (t80) cc_final: 0.7622 (t80) REVERT: D 56 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8376 (mmtm) REVERT: D 60 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8042 (ptp-170) REVERT: D 73 ILE cc_start: 0.5414 (OUTLIER) cc_final: 0.4863 (tp) REVERT: D 88 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6857 (mt-10) REVERT: D 102 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.5692 (pm20) REVERT: D 116 ILE cc_start: 0.7768 (pt) cc_final: 0.7383 (tp) outliers start: 38 outliers final: 18 residues processed: 135 average time/residue: 0.0880 time to fit residues: 15.4045 Evaluate side-chains 132 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 13 optimal weight: 0.0570 chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 40.0000 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 126 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 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 = 0.4510 r_free = 0.4510 target = 0.212070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.164504 restraints weight = 7798.277| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.52 r_work: 0.3781 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6457 Z= 0.155 Angle : 0.674 12.309 8871 Z= 0.366 Chirality : 0.046 0.222 952 Planarity : 0.004 0.053 986 Dihedral : 23.882 158.928 1232 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 6.13 % Allowed : 31.52 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.33), residues: 635 helix: -0.13 (0.33), residues: 234 sheet: -1.54 (0.52), residues: 98 loop : -1.83 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 180 TYR 0.020 0.001 TYR D 103 PHE 0.014 0.001 PHE A 250 TRP 0.011 0.001 TRP D 70 HIS 0.003 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 6457) covalent geometry : angle 0.67407 / 0.37 ( 8871) hydrogen bonds : bond 0.05462 / 3.37 ( 230) hydrogen bonds : angle 4.72845 / 3.44 ( 620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.242 Fit side-chains REVERT: A 257 LYS cc_start: 0.7462 (mmtm) cc_final: 0.7199 (mmmm) REVERT: A 275 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6014 (mt-10) REVERT: B 66 THR cc_start: 0.8273 (m) cc_final: 0.8030 (p) REVERT: B 71 TYR cc_start: 0.7942 (p90) cc_final: 0.7399 (p90) REVERT: B 116 LYS cc_start: 0.7607 (mmmt) cc_final: 0.7175 (tptp) REVERT: B 153 ILE cc_start: 0.6350 (OUTLIER) cc_final: 0.6008 (pp) REVERT: C 180 ARG cc_start: 0.7741 (tmm-80) cc_final: 0.7519 (tmm-80) REVERT: C 184 GLN cc_start: 0.4405 (OUTLIER) cc_final: 0.3706 (pm20) REVERT: D 41 TYR cc_start: 0.8000 (t80) cc_final: 0.7732 (t80) REVERT: D 56 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8357 (mmtm) REVERT: D 60 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8027 (ptp-170) REVERT: D 73 ILE cc_start: 0.5388 (OUTLIER) cc_final: 0.4852 (tp) REVERT: D 88 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6796 (mt-10) REVERT: D 102 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.5738 (pm20) REVERT: D 116 ILE cc_start: 0.7726 (pt) cc_final: 0.7383 (tp) outliers start: 36 outliers final: 22 residues processed: 134 average time/residue: 0.0935 time to fit residues: 16.0994 Evaluate side-chains 138 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.0070 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 30.0000 chunk 57 optimal weight: 6.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** D 133 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 = 0.4512 r_free = 0.4512 target = 0.212369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.165108 restraints weight = 7834.627| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.46 r_work: 0.3787 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6457 Z= 0.147 Angle : 0.665 11.545 8871 Z= 0.362 Chirality : 0.045 0.250 952 Planarity : 0.003 0.047 986 Dihedral : 23.829 159.174 1230 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 6.64 % Allowed : 30.66 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.33), residues: 635 helix: -0.04 (0.33), residues: 234 sheet: -1.52 (0.52), residues: 98 loop : -1.79 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.016 0.001 TYR D 103 PHE 0.013 0.001 PHE A 250 TRP 0.009 0.001 TRP D 70 HIS 0.002 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 6457) covalent geometry : angle 0.66511 / 0.36 ( 8871) hydrogen bonds : bond 0.05179 / 3.20 ( 230) hydrogen bonds : angle 4.69921 / 3.44 ( 620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5902 (mt-10) REVERT: B 66 THR cc_start: 0.8256 (m) cc_final: 0.8028 (p) REVERT: B 71 TYR cc_start: 0.7908 (p90) cc_final: 0.7366 (p90) REVERT: B 116 LYS cc_start: 0.7562 (mmmt) cc_final: 0.7194 (tptp) REVERT: B 153 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.6012 (pp) REVERT: C 174 LYS cc_start: 0.8436 (ptpp) cc_final: 0.8184 (ptpp) REVERT: D 41 TYR cc_start: 0.7973 (t80) cc_final: 0.7739 (t80) REVERT: D 56 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8352 (mmtm) REVERT: D 60 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8022 (ptp-170) REVERT: D 73 ILE cc_start: 0.5343 (OUTLIER) cc_final: 0.4801 (tp) REVERT: D 88 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6688 (mt-10) REVERT: D 102 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5757 (pm20) REVERT: D 116 ILE cc_start: 0.7761 (pt) cc_final: 0.7414 (tp) outliers start: 39 outliers final: 25 residues processed: 135 average time/residue: 0.0918 time to fit residues: 15.9748 Evaluate side-chains 134 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 3 optimal weight: 0.0980 chunk 41 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 63 optimal weight: 30.0000 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 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 = 0.4525 r_free = 0.4525 target = 0.213627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.166410 restraints weight = 7792.380| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.44 r_work: 0.3803 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6457 Z= 0.136 Angle : 0.657 11.121 8871 Z= 0.357 Chirality : 0.045 0.211 952 Planarity : 0.004 0.045 986 Dihedral : 23.780 159.430 1230 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.96 % Allowed : 30.83 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.33), residues: 635 helix: -0.03 (0.33), residues: 235 sheet: -1.46 (0.53), residues: 98 loop : -1.75 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.011 0.001 TYR D 103 PHE 0.011 0.001 PHE B 259 TRP 0.008 0.001 TRP D 70 HIS 0.002 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 6457) covalent geometry : angle 0.65697 / 0.36 ( 8871) hydrogen bonds : bond 0.04944 / 3.08 ( 230) hydrogen bonds : angle 4.66572 / 3.42 ( 620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5865 (mt-10) REVERT: B 66 THR cc_start: 0.8249 (m) cc_final: 0.8036 (p) REVERT: B 71 TYR cc_start: 0.7887 (p90) cc_final: 0.7351 (p90) REVERT: B 116 LYS cc_start: 0.7584 (mmmt) cc_final: 0.7200 (tptp) REVERT: B 153 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.5986 (pp) REVERT: C 174 LYS cc_start: 0.8362 (ptpp) cc_final: 0.8157 (ptpp) REVERT: D 41 TYR cc_start: 0.7956 (t80) cc_final: 0.7719 (t80) REVERT: D 60 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7923 (ptp-170) REVERT: D 73 ILE cc_start: 0.5375 (OUTLIER) cc_final: 0.4852 (tp) REVERT: D 102 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5724 (pm20) REVERT: D 116 ILE cc_start: 0.7758 (pt) cc_final: 0.7413 (tp) outliers start: 35 outliers final: 25 residues processed: 124 average time/residue: 0.0903 time to fit residues: 14.5892 Evaluate side-chains 130 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.0030 chunk 54 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** D 133 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 = 0.4519 r_free = 0.4519 target = 0.212942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.166367 restraints weight = 7717.678| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.49 r_work: 0.3806 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6457 Z= 0.145 Angle : 0.666 13.283 8871 Z= 0.360 Chirality : 0.045 0.207 952 Planarity : 0.004 0.044 986 Dihedral : 23.742 159.172 1230 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 6.47 % Allowed : 30.49 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.33), residues: 635 helix: 0.03 (0.33), residues: 235 sheet: -1.67 (0.50), residues: 108 loop : -1.71 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.009 0.001 TYR D 103 PHE 0.013 0.001 PHE A 250 TRP 0.007 0.001 TRP D 70 HIS 0.002 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 6457) covalent geometry : angle 0.66643 / 0.36 ( 8871) hydrogen bonds : bond 0.04830 / 3.01 ( 230) hydrogen bonds : angle 4.63562 / 3.39 ( 620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.5865 (mt-10) REVERT: B 66 THR cc_start: 0.8243 (m) cc_final: 0.8037 (p) REVERT: B 71 TYR cc_start: 0.7911 (p90) cc_final: 0.7370 (p90) REVERT: B 116 LYS cc_start: 0.7572 (mmmt) cc_final: 0.7193 (tptp) REVERT: B 153 ILE cc_start: 0.6301 (OUTLIER) cc_final: 0.5993 (pp) REVERT: D 41 TYR cc_start: 0.7968 (t80) cc_final: 0.7721 (t80) REVERT: D 60 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7941 (ptp-170) REVERT: D 73 ILE cc_start: 0.5172 (OUTLIER) cc_final: 0.4624 (tp) REVERT: D 102 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5737 (pm20) REVERT: D 116 ILE cc_start: 0.7746 (pt) cc_final: 0.7393 (tp) outliers start: 38 outliers final: 24 residues processed: 125 average time/residue: 0.0871 time to fit residues: 14.2115 Evaluate side-chains 125 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 38 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 133 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 = 0.4519 r_free = 0.4519 target = 0.212979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.166705 restraints weight = 7824.866| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.68 r_work: 0.3792 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6457 Z= 0.151 Angle : 0.708 16.351 8871 Z= 0.376 Chirality : 0.045 0.269 952 Planarity : 0.004 0.042 986 Dihedral : 23.736 159.248 1230 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.45 % Allowed : 31.35 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.33), residues: 635 helix: 0.05 (0.33), residues: 235 sheet: -1.70 (0.49), residues: 108 loop : -1.69 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.016 0.001 TYR D 103 PHE 0.012 0.001 PHE A 250 TRP 0.007 0.001 TRP D 70 HIS 0.002 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6457) covalent geometry : angle 0.70792 / 0.38 ( 8871) hydrogen bonds : bond 0.04786 / 2.99 ( 230) hydrogen bonds : angle 4.70626 / 3.43 ( 620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.5886 (mt-10) REVERT: B 71 TYR cc_start: 0.7911 (p90) cc_final: 0.7355 (p90) REVERT: B 116 LYS cc_start: 0.7606 (mmmt) cc_final: 0.7216 (tptp) REVERT: B 153 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.6016 (pp) REVERT: B 204 GLN cc_start: 0.7541 (tp40) cc_final: 0.6623 (tp-100) REVERT: C 184 GLN cc_start: 0.4341 (OUTLIER) cc_final: 0.3943 (pm20) REVERT: D 41 TYR cc_start: 0.7984 (t80) cc_final: 0.7741 (t80) REVERT: D 56 LYS cc_start: 0.9102 (mmmm) cc_final: 0.8319 (mmtm) REVERT: D 60 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7973 (ptp-170) REVERT: D 73 ILE cc_start: 0.5304 (OUTLIER) cc_final: 0.4749 (tp) REVERT: D 102 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5717 (pm20) REVERT: D 116 ILE cc_start: 0.7754 (pt) cc_final: 0.7399 (tp) outliers start: 32 outliers final: 23 residues processed: 120 average time/residue: 0.0829 time to fit residues: 12.8473 Evaluate side-chains 133 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 23 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 63 optimal weight: 30.0000 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 133 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 = 0.4507 r_free = 0.4507 target = 0.211573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.164912 restraints weight = 7782.992| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.58 r_work: 0.3778 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6457 Z= 0.156 Angle : 0.713 15.914 8871 Z= 0.378 Chirality : 0.046 0.259 952 Planarity : 0.003 0.038 986 Dihedral : 23.719 158.993 1230 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 5.11 % Allowed : 31.69 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.33), residues: 635 helix: 0.11 (0.33), residues: 235 sheet: -1.64 (0.51), residues: 98 loop : -1.75 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.010 0.001 TYR D 103 PHE 0.014 0.001 PHE A 250 TRP 0.007 0.001 TRP D 70 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 6457) covalent geometry : angle 0.71278 / 0.38 ( 8871) hydrogen bonds : bond 0.04676 / 2.92 ( 230) hydrogen bonds : angle 4.65474 / 3.39 ( 620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.5819 (mt-10) REVERT: B 71 TYR cc_start: 0.7911 (p90) cc_final: 0.7351 (p90) REVERT: B 116 LYS cc_start: 0.7706 (mmmt) cc_final: 0.7328 (tptp) REVERT: B 153 ILE cc_start: 0.6350 (OUTLIER) cc_final: 0.6041 (pp) REVERT: B 204 GLN cc_start: 0.7526 (tp40) cc_final: 0.6739 (tp-100) REVERT: C 184 GLN cc_start: 0.4156 (OUTLIER) cc_final: 0.3779 (pm20) REVERT: D 41 TYR cc_start: 0.8005 (t80) cc_final: 0.7740 (t80) REVERT: D 56 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8624 (mmtm) REVERT: D 73 ILE cc_start: 0.5399 (OUTLIER) cc_final: 0.4827 (tp) REVERT: D 102 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5635 (pm20) REVERT: D 106 LYS cc_start: 0.6339 (pttm) cc_final: 0.5142 (tptp) REVERT: D 116 ILE cc_start: 0.7759 (pt) cc_final: 0.7398 (tp) outliers start: 30 outliers final: 23 residues processed: 123 average time/residue: 0.0765 time to fit residues: 12.3908 Evaluate side-chains 129 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 50 optimal weight: 0.0060 chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 40.0000 chunk 24 optimal weight: 4.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.4520 r_free = 0.4520 target = 0.213000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.166595 restraints weight = 7740.187| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.57 r_work: 0.3801 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6457 Z= 0.144 Angle : 0.704 15.345 8871 Z= 0.374 Chirality : 0.046 0.341 952 Planarity : 0.003 0.037 986 Dihedral : 23.666 159.475 1230 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.11 % Allowed : 32.03 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.48 (0.34), residues: 635 helix: 0.21 (0.33), residues: 235 sheet: -1.75 (0.49), residues: 108 loop : -1.62 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.009 0.001 TYR D 103 PHE 0.013 0.001 PHE B 156 TRP 0.010 0.001 TRP D 70 HIS 0.002 0.001 HIS D 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6457) covalent geometry : angle 0.70386 / 0.37 ( 8871) hydrogen bonds : bond 0.04400 / 2.76 ( 230) hydrogen bonds : angle 4.65408 / 3.39 ( 620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.5781 (mt-10) REVERT: B 71 TYR cc_start: 0.7912 (p90) cc_final: 0.7362 (p90) REVERT: B 116 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7364 (tptp) REVERT: B 153 ILE cc_start: 0.6341 (OUTLIER) cc_final: 0.6014 (pp) REVERT: B 204 GLN cc_start: 0.7500 (tp40) cc_final: 0.6673 (tp-100) REVERT: C 184 GLN cc_start: 0.4154 (OUTLIER) cc_final: 0.3786 (pm20) REVERT: D 41 TYR cc_start: 0.7964 (t80) cc_final: 0.7741 (t80) REVERT: D 56 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8280 (mmtm) REVERT: D 60 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7980 (ptp-170) REVERT: D 73 ILE cc_start: 0.5413 (OUTLIER) cc_final: 0.4857 (tp) REVERT: D 102 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.5602 (pm20) REVERT: D 106 LYS cc_start: 0.6369 (pttm) cc_final: 0.5201 (tptp) REVERT: D 116 ILE cc_start: 0.7731 (pt) cc_final: 0.7414 (tp) outliers start: 30 outliers final: 23 residues processed: 126 average time/residue: 0.0880 time to fit residues: 14.3256 Evaluate side-chains 129 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 161 PHE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 102 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 7 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 214 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 = 0.4514 r_free = 0.4514 target = 0.212237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.164682 restraints weight = 7752.515| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.61 r_work: 0.3782 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6457 Z= 0.163 Angle : 0.755 17.428 8871 Z= 0.395 Chirality : 0.047 0.323 952 Planarity : 0.003 0.035 986 Dihedral : 23.658 158.993 1230 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 5.11 % Allowed : 32.37 % Favored : 62.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.34), residues: 635 helix: 0.15 (0.33), residues: 235 sheet: -1.78 (0.48), residues: 108 loop : -1.60 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.011 0.001 TYR B 152 PHE 0.012 0.001 PHE B 259 TRP 0.040 0.002 TRP D 70 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 6457) covalent geometry : angle 0.75478 / 0.39 ( 8871) hydrogen bonds : bond 0.04458 / 2.81 ( 230) hydrogen bonds : angle 4.70645 / 3.43 ( 620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1657.39 seconds wall clock time: 29 minutes 5.29 seconds (1745.29 seconds total)