Starting phenix.real_space_refine on Thu Jul 2 07:48:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9c_49165/07_2026/9n9c_49165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9c_49165/07_2026/9n9c_49165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n9c_49165/07_2026/9n9c_49165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9c_49165/07_2026/9n9c_49165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n9c_49165/07_2026/9n9c_49165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9c_49165/07_2026/9n9c_49165.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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: 6 Type Number sf(0) Gaussians P 88 5.49 5 Mg 1 5.21 5 S 30 5.16 5 C 4520 2.51 5 N 1353 2.21 5 O 1610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 7602 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2860 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 338} Chain breaks: 2 Chain: "B" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2860 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 338} Chain breaks: 1 Chain: "c" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1881 Classifications: {'RNA': 88} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 44, 'rna3p_pyr': 35} Link IDs: {'rna2p': 9, 'rna3p': 78} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.60, per 1000 atoms: 0.21 Number of scatterers: 7602 At special positions: 0 Unit cell: (84.666, 107.682, 100.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 88 15.00 Mg 1 11.99 O 1610 8.00 N 1353 7.00 C 4520 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 268.0 milliseconds 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1308 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 6 sheets defined 48.0% alpha, 25.0% beta 25 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 20 through 63 removed outlier: 3.835A pdb=" N LYS A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 96 Processing helix chain 'A' and resid 102 through 119 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.677A pdb=" N LYS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 270 removed outlier: 4.308A pdb=" N TYR A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 4.246A pdb=" N ARG A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 315 removed outlier: 4.236A pdb=" N TYR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 3.900A pdb=" N TYR A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 54 Processing helix chain 'B' and resid 84 through 96 removed outlier: 4.207A pdb=" N THR B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 126 removed outlier: 3.612A pdb=" N LEU B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLN B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 248 through 272 removed outlier: 4.713A pdb=" N ARG B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 315 removed outlier: 5.396A pdb=" N ALA B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL B 286 " --> pdb=" O LYS B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 removed outlier: 4.137A pdb=" N ILE A 204 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE A 158 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 157 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR A 151 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N CYS A 159 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 149 " --> pdb=" O CYS A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 141 removed outlier: 4.636A pdb=" N LYS A 191 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 246 removed outlier: 3.604A pdb=" N ILE A 235 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA A 317 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL A 223 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 319 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 225 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 321 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A 323 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.732A pdb=" N SER B 195 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 204 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N PHE B 158 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 157 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TYR B 151 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS B 159 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU B 149 " --> pdb=" O CYS B 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.732A pdb=" N SER B 195 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 242 through 246 removed outlier: 3.755A pdb=" N ILE B 235 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ALA B 317 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL B 223 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY B 318 " --> pdb=" O GLU B 361 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE B 363 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 320 " --> pdb=" O ILE B 363 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLY B 365 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 322 " --> pdb=" O GLY B 365 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 1014 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1801 1.33 - 1.45: 2023 1.45 - 1.57: 3884 1.57 - 1.69: 175 1.69 - 1.81: 52 Bond restraints: 7935 Sorted by residual: bond pdb=" N7 G c 29 " pdb=" C5 G c 29 " ideal model delta sigma weight residual 1.388 1.373 0.015 6.00e-03 2.78e+04 6.41e+00 bond pdb=" N9 A c 46 " pdb=" C4 A c 46 " ideal model delta sigma weight residual 1.374 1.359 0.015 6.00e-03 2.78e+04 6.24e+00 bond pdb=" C5 G c 27 " pdb=" C4 G c 27 " ideal model delta sigma weight residual 1.379 1.363 0.016 7.00e-03 2.04e+04 5.37e+00 bond pdb=" C5 G c 6 " pdb=" C4 G c 6 " ideal model delta sigma weight residual 1.379 1.363 0.016 7.00e-03 2.04e+04 4.99e+00 bond pdb=" N3 C c 13 " pdb=" C4 C c 13 " ideal model delta sigma weight residual 1.335 1.321 0.014 7.00e-03 2.04e+04 4.18e+00 ... (remaining 7930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 11000 2.68 - 5.36: 71 5.36 - 8.03: 8 8.03 - 10.71: 1 10.71 - 13.39: 1 Bond angle restraints: 11081 Sorted by residual: angle pdb=" C1' U c 30 " pdb=" N1 U c 30 " pdb=" C2 U c 30 " ideal model delta sigma weight residual 117.70 122.77 -5.07 1.20e+00 6.94e-01 1.78e+01 angle pdb=" C1' C c 13 " pdb=" N1 C c 13 " pdb=" C2 C c 13 " ideal model delta sigma weight residual 118.80 123.35 -4.55 1.10e+00 8.26e-01 1.71e+01 angle pdb=" O2 C c 45 " pdb=" C2 C c 45 " pdb=" N3 C c 45 " ideal model delta sigma weight residual 121.90 119.20 2.70 7.00e-01 2.04e+00 1.49e+01 angle pdb=" O2 C c 13 " pdb=" C2 C c 13 " pdb=" N3 C c 13 " ideal model delta sigma weight residual 121.90 119.36 2.54 7.00e-01 2.04e+00 1.31e+01 angle pdb=" N1 C c 13 " pdb=" C2 C c 13 " pdb=" O2 C c 13 " ideal model delta sigma weight residual 118.90 121.03 -2.13 6.00e-01 2.78e+00 1.26e+01 ... (remaining 11076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.72: 4507 32.72 - 65.45: 362 65.45 - 98.17: 28 98.17 - 130.89: 0 130.89 - 163.62: 1 Dihedral angle restraints: 4898 sinusoidal: 2869 harmonic: 2029 Sorted by residual: dihedral pdb=" O4' C c 13 " pdb=" C1' C c 13 " pdb=" N1 C c 13 " pdb=" C2 C c 13 " ideal model delta sinusoidal sigma weight residual 200.00 36.38 163.62 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" CA MET B 85 " pdb=" C MET B 85 " pdb=" N ASN B 86 " pdb=" CA ASN B 86 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA TYR A 272 " pdb=" C TYR A 272 " pdb=" N SER A 273 " pdb=" CA SER A 273 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 4895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 808 0.032 - 0.063: 343 0.063 - 0.095: 78 0.095 - 0.127: 45 0.127 - 0.158: 10 Chirality restraints: 1284 Sorted by residual: chirality pdb=" CB THR B 292 " pdb=" CA THR B 292 " pdb=" OG1 THR B 292 " pdb=" CG2 THR B 292 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CB ILE B 14 " pdb=" CA ILE B 14 " pdb=" CG1 ILE B 14 " pdb=" CG2 ILE B 14 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE B 246 " pdb=" N ILE B 246 " pdb=" C ILE B 246 " pdb=" CB ILE B 246 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1281 not shown) Planarity restraints: 1057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G c 28 " -0.061 2.00e-02 2.50e+03 2.64e-02 2.09e+01 pdb=" N9 G c 28 " 0.064 2.00e-02 2.50e+03 pdb=" C8 G c 28 " 0.008 2.00e-02 2.50e+03 pdb=" N7 G c 28 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G c 28 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G c 28 " -0.014 2.00e-02 2.50e+03 pdb=" O6 G c 28 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G c 28 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G c 28 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G c 28 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G c 28 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G c 28 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 184 " 0.255 9.50e-02 1.11e+02 1.15e-01 8.37e+00 pdb=" NE ARG B 184 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 184 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 184 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 184 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A c 53 " -0.024 2.00e-02 2.50e+03 1.20e-02 3.95e+00 pdb=" N9 A c 53 " 0.031 2.00e-02 2.50e+03 pdb=" C8 A c 53 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A c 53 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A c 53 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A c 53 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A c 53 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A c 53 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A c 53 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A c 53 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A c 53 " -0.001 2.00e-02 2.50e+03 ... (remaining 1054 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 109 2.64 - 3.20: 6572 3.20 - 3.77: 12627 3.77 - 4.33: 16647 4.33 - 4.90: 25229 Nonbonded interactions: 61184 Sorted by model distance: nonbonded pdb=" N2 G c 16 " pdb=" O2 C c 71 " model vdw 2.073 2.496 nonbonded pdb=" NH1 ARG A 10 " pdb=" OP2 U c 75 " model vdw 2.136 3.120 nonbonded pdb=" O GLU A 251 " pdb=" OH TYR A 296 " model vdw 2.149 3.040 nonbonded pdb=" ND2 ASN A 43 " pdb=" O GLU B 127 " model vdw 2.214 3.120 nonbonded pdb=" O2' C c 23 " pdb=" N3 A c 53 " model vdw 2.248 3.120 ... (remaining 61179 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.380 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: 0.240 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.680 Find NCS groups from input model: 0.060 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 0.057 7935 Z= 0.302 Angle : 0.625 13.388 11081 Z= 0.405 Chirality : 0.040 0.158 1284 Planarity : 0.005 0.115 1057 Dihedral : 19.867 163.616 3590 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.43 % Favored : 94.13 % Rotamer: Outliers : 3.88 % Allowed : 27.51 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.32), residues: 682 helix: 1.29 (0.29), residues: 319 sheet: -0.66 (0.50), residues: 113 loop : -2.25 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 184 TYR 0.012 0.001 TYR B 254 PHE 0.021 0.002 PHE A 39 TRP 0.026 0.002 TRP B 342 HIS 0.005 0.001 HIS B 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.30 ( 7935) covalent geometry : angle 0.62473 / 0.41 (11081) hydrogen bonds : bond 0.13996 / 8.97 ( 396) hydrogen bonds : angle 5.71326 / 4.24 ( 1126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7458 (m-30) cc_final: 0.7162 (m-30) REVERT: A 53 GLU cc_start: 0.7394 (tt0) cc_final: 0.5945 (tt0) REVERT: A 130 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6565 (mp) REVERT: A 134 LYS cc_start: 0.7435 (mmtt) cc_final: 0.7193 (mmtt) REVERT: A 174 ASP cc_start: 0.7733 (t0) cc_final: 0.7271 (t0) REVERT: A 184 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7229 (mtp85) REVERT: A 263 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7542 (ttm170) REVERT: B 57 ASP cc_start: 0.6885 (m-30) cc_final: 0.6617 (m-30) REVERT: B 91 VAL cc_start: 0.7885 (t) cc_final: 0.7640 (p) REVERT: B 100 MET cc_start: 0.4754 (tpt) cc_final: 0.3979 (tpt) REVERT: B 139 PHE cc_start: 0.7723 (p90) cc_final: 0.7273 (p90) REVERT: B 223 VAL cc_start: 0.8678 (p) cc_final: 0.8352 (m) REVERT: B 231 LEU cc_start: 0.8798 (mt) cc_final: 0.8591 (mt) REVERT: B 232 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6954 (mm-30) REVERT: B 241 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7703 (tmtt) REVERT: B 342 TRP cc_start: 0.8414 (m100) cc_final: 0.8154 (m100) outliers start: 24 outliers final: 21 residues processed: 148 average time/residue: 0.1017 time to fit residues: 18.8972 Evaluate side-chains 158 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 164 ARG Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 HIS ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4263 r_free = 0.4263 target = 0.184761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.152362 restraints weight = 11057.446| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.33 r_work: 0.3744 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7935 Z= 0.157 Angle : 0.536 11.626 11081 Z= 0.295 Chirality : 0.038 0.178 1284 Planarity : 0.004 0.041 1057 Dihedral : 19.137 161.282 2157 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.69 % Favored : 94.87 % Rotamer: Outliers : 5.99 % Allowed : 24.92 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.11 (0.32), residues: 682 helix: 1.68 (0.28), residues: 317 sheet: -0.84 (0.47), residues: 124 loop : -2.08 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 184 TYR 0.010 0.001 TYR B 344 PHE 0.018 0.002 PHE A 39 TRP 0.009 0.001 TRP B 342 HIS 0.006 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 ( 7935) covalent geometry : angle 0.53599 / 0.29 (11081) hydrogen bonds : bond 0.05829 / 4.00 ( 396) hydrogen bonds : angle 4.59827 / 3.38 ( 1126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7367 (tt0) cc_final: 0.5858 (tt0) REVERT: A 130 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6606 (mp) REVERT: A 134 LYS cc_start: 0.7406 (mmtt) cc_final: 0.7163 (mmtt) REVERT: A 180 MET cc_start: 0.6889 (mmt) cc_final: 0.6579 (mmt) REVERT: A 184 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7470 (mtm-85) REVERT: A 214 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8166 (ptpt) REVERT: A 263 ARG cc_start: 0.7786 (ttp80) cc_final: 0.7547 (ttm170) REVERT: A 280 LYS cc_start: 0.7934 (tttt) cc_final: 0.7640 (mttt) REVERT: B 57 ASP cc_start: 0.6896 (m-30) cc_final: 0.6607 (m-30) REVERT: B 91 VAL cc_start: 0.7886 (t) cc_final: 0.7644 (p) REVERT: B 139 PHE cc_start: 0.7719 (p90) cc_final: 0.7217 (p90) REVERT: B 146 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5815 (tt) REVERT: B 191 LYS cc_start: 0.7191 (tttt) cc_final: 0.6939 (tttm) REVERT: B 231 LEU cc_start: 0.8763 (mt) cc_final: 0.8558 (tp) REVERT: B 232 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6874 (mm-30) REVERT: B 241 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7667 (tmtt) REVERT: B 342 TRP cc_start: 0.8479 (m100) cc_final: 0.8128 (m100) outliers start: 37 outliers final: 20 residues processed: 151 average time/residue: 0.0995 time to fit residues: 18.9278 Evaluate side-chains 154 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 5.9990 chunk 20 optimal weight: 0.0770 chunk 58 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 42 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.186558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.154235 restraints weight = 11040.265| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.33 r_work: 0.3770 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7935 Z= 0.111 Angle : 0.482 10.977 11081 Z= 0.265 Chirality : 0.037 0.172 1284 Planarity : 0.003 0.038 1057 Dihedral : 18.905 159.972 2132 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.40 % Favored : 95.16 % Rotamer: Outliers : 5.66 % Allowed : 25.57 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.32), residues: 682 helix: 1.95 (0.27), residues: 317 sheet: -0.81 (0.47), residues: 126 loop : -1.88 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 184 TYR 0.015 0.001 TYR B 353 PHE 0.014 0.001 PHE A 39 TRP 0.005 0.001 TRP A 124 HIS 0.004 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 ( 7935) covalent geometry : angle 0.48246 / 0.27 (11081) hydrogen bonds : bond 0.05132 / 3.54 ( 396) hydrogen bonds : angle 4.23894 / 3.12 ( 1126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7279 (ptmt) cc_final: 0.6904 (ttpp) REVERT: A 53 GLU cc_start: 0.7271 (tt0) cc_final: 0.5820 (tt0) REVERT: A 134 LYS cc_start: 0.7376 (mmtt) cc_final: 0.7124 (mmtt) REVERT: A 180 MET cc_start: 0.6952 (mmt) cc_final: 0.6744 (mmt) REVERT: A 184 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7407 (mtm-85) REVERT: A 214 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8122 (ptpt) REVERT: A 263 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7458 (ttm170) REVERT: A 280 LYS cc_start: 0.7927 (tttt) cc_final: 0.7648 (mttt) REVERT: B 57 ASP cc_start: 0.6847 (m-30) cc_final: 0.6571 (m-30) REVERT: B 91 VAL cc_start: 0.7873 (t) cc_final: 0.7638 (p) REVERT: B 139 PHE cc_start: 0.7678 (p90) cc_final: 0.7197 (p90) REVERT: B 191 LYS cc_start: 0.7070 (tttt) cc_final: 0.6840 (tttm) REVERT: B 232 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6824 (mm-30) REVERT: B 241 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7650 (tmtt) REVERT: B 342 TRP cc_start: 0.8495 (m100) cc_final: 0.8290 (m100) outliers start: 35 outliers final: 22 residues processed: 152 average time/residue: 0.0990 time to fit residues: 18.7885 Evaluate side-chains 151 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 349 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 59 optimal weight: 40.0000 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4224 r_free = 0.4224 target = 0.181285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.148135 restraints weight = 11141.735| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.39 r_work: 0.3692 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 7935 Z= 0.335 Angle : 0.618 11.647 11081 Z= 0.340 Chirality : 0.045 0.175 1284 Planarity : 0.005 0.046 1057 Dihedral : 18.892 163.656 2127 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.28 % Favored : 94.28 % Rotamer: Outliers : 7.61 % Allowed : 24.60 % Favored : 67.80 % 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: -0.26 (0.31), residues: 682 helix: 1.52 (0.27), residues: 311 sheet: -1.06 (0.45), residues: 126 loop : -1.92 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 184 TYR 0.016 0.002 TYR B 353 PHE 0.029 0.003 PHE A 139 TRP 0.010 0.002 TRP A 206 HIS 0.008 0.002 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.34 ( 7935) covalent geometry : angle 0.61763 / 0.34 (11081) hydrogen bonds : bond 0.06099 / 4.18 ( 396) hydrogen bonds : angle 4.51657 / 3.32 ( 1126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7471 (tt0) cc_final: 0.5882 (tt0) REVERT: A 134 LYS cc_start: 0.7474 (mmtt) cc_final: 0.7219 (mmtt) REVERT: A 136 ASP cc_start: 0.7490 (p0) cc_final: 0.7202 (p0) REVERT: A 180 MET cc_start: 0.6981 (mmt) cc_final: 0.6680 (mmt) REVERT: A 184 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7465 (mtm-85) REVERT: A 214 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8221 (ptpt) REVERT: A 263 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7605 (ttm170) REVERT: A 280 LYS cc_start: 0.8013 (tttt) cc_final: 0.7771 (mttt) REVERT: B 57 ASP cc_start: 0.6985 (m-30) cc_final: 0.6716 (m-30) REVERT: B 91 VAL cc_start: 0.7903 (t) cc_final: 0.7671 (p) REVERT: B 139 PHE cc_start: 0.7746 (p90) cc_final: 0.7271 (p90) REVERT: B 146 ILE cc_start: 0.6202 (OUTLIER) cc_final: 0.5928 (tt) REVERT: B 191 LYS cc_start: 0.7143 (tttt) cc_final: 0.6934 (tttm) REVERT: B 198 GLN cc_start: 0.7441 (tm-30) cc_final: 0.6946 (tm-30) REVERT: B 232 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6938 (mm-30) REVERT: B 241 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7784 (tmtt) outliers start: 47 outliers final: 32 residues processed: 157 average time/residue: 0.1246 time to fit residues: 24.5289 Evaluate side-chains 167 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4266 r_free = 0.4266 target = 0.185435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.152807 restraints weight = 11051.314| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.34 r_work: 0.3749 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7935 Z= 0.141 Angle : 0.501 11.034 11081 Z= 0.276 Chirality : 0.038 0.206 1284 Planarity : 0.004 0.046 1057 Dihedral : 18.944 161.022 2127 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.40 % Favored : 95.16 % Rotamer: Outliers : 5.66 % Allowed : 26.70 % Favored : 67.64 % 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: 0.14 (0.32), residues: 682 helix: 1.89 (0.27), residues: 312 sheet: -0.80 (0.47), residues: 124 loop : -1.82 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 184 TYR 0.015 0.001 TYR B 353 PHE 0.017 0.002 PHE A 39 TRP 0.009 0.001 TRP B 342 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 7935) covalent geometry : angle 0.50051 / 0.28 (11081) hydrogen bonds : bond 0.05209 / 3.60 ( 396) hydrogen bonds : angle 4.23334 / 3.12 ( 1126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7401 (tt0) cc_final: 0.5843 (tt0) REVERT: A 134 LYS cc_start: 0.7381 (mmtt) cc_final: 0.7115 (mmtt) REVERT: A 136 ASP cc_start: 0.7448 (p0) cc_final: 0.7179 (p0) REVERT: A 180 MET cc_start: 0.6899 (mmt) cc_final: 0.6602 (mmt) REVERT: A 184 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7170 (mtp85) REVERT: A 214 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8173 (ptpt) REVERT: A 263 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7535 (ttm170) REVERT: B 57 ASP cc_start: 0.6814 (m-30) cc_final: 0.6563 (m-30) REVERT: B 91 VAL cc_start: 0.7906 (t) cc_final: 0.7674 (p) REVERT: B 139 PHE cc_start: 0.7714 (p90) cc_final: 0.7237 (p90) REVERT: B 198 GLN cc_start: 0.7417 (tm-30) cc_final: 0.7012 (tm-30) REVERT: B 232 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6757 (mm-30) REVERT: B 238 LYS cc_start: 0.7015 (tppt) cc_final: 0.6795 (mtpp) REVERT: B 241 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7652 (tmtt) REVERT: B 315 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.7133 (m-70) outliers start: 35 outliers final: 24 residues processed: 153 average time/residue: 0.1304 time to fit residues: 24.7215 Evaluate side-chains 157 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 349 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 71 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 65 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 59 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 HIS ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4260 r_free = 0.4260 target = 0.184814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.152235 restraints weight = 11109.318| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.32 r_work: 0.3743 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7935 Z= 0.158 Angle : 0.494 11.000 11081 Z= 0.274 Chirality : 0.038 0.205 1284 Planarity : 0.003 0.044 1057 Dihedral : 18.889 161.433 2127 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.99 % Favored : 94.57 % Rotamer: Outliers : 5.99 % Allowed : 26.38 % Favored : 67.64 % 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: 0.14 (0.32), residues: 682 helix: 1.93 (0.27), residues: 312 sheet: -0.88 (0.47), residues: 126 loop : -1.85 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 184 TYR 0.015 0.001 TYR B 353 PHE 0.017 0.002 PHE A 39 TRP 0.007 0.001 TRP B 342 HIS 0.010 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 ( 7935) covalent geometry : angle 0.49424 / 0.27 (11081) hydrogen bonds : bond 0.05158 / 3.56 ( 396) hydrogen bonds : angle 4.19482 / 3.10 ( 1126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7297 (ptmt) cc_final: 0.6877 (ttpp) REVERT: A 53 GLU cc_start: 0.7425 (tt0) cc_final: 0.5868 (tt0) REVERT: A 134 LYS cc_start: 0.7407 (mmtt) cc_final: 0.7150 (mmtt) REVERT: A 136 ASP cc_start: 0.7441 (p0) cc_final: 0.7178 (p0) REVERT: A 180 MET cc_start: 0.6906 (mmt) cc_final: 0.6603 (mmt) REVERT: A 184 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7465 (mtm-85) REVERT: A 214 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8180 (ptpt) REVERT: A 263 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7531 (ttm170) REVERT: A 280 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7766 (ttmm) REVERT: B 57 ASP cc_start: 0.6850 (m-30) cc_final: 0.6598 (m-30) REVERT: B 91 VAL cc_start: 0.7912 (t) cc_final: 0.7682 (p) REVERT: B 139 PHE cc_start: 0.7705 (p90) cc_final: 0.7225 (p90) REVERT: B 198 GLN cc_start: 0.7411 (tm-30) cc_final: 0.7015 (tm-30) REVERT: B 232 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6819 (mm-30) REVERT: B 238 LYS cc_start: 0.7041 (tppt) cc_final: 0.6827 (mtpp) REVERT: B 241 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7710 (tmtt) REVERT: B 315 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.7158 (m-70) outliers start: 37 outliers final: 32 residues processed: 148 average time/residue: 0.1349 time to fit residues: 24.8270 Evaluate side-chains 165 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 356 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 73 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 59 optimal weight: 40.0000 chunk 53 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4227 r_free = 0.4227 target = 0.181599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.148761 restraints weight = 10999.116| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.35 r_work: 0.3698 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7935 Z= 0.296 Angle : 0.603 11.666 11081 Z= 0.331 Chirality : 0.044 0.237 1284 Planarity : 0.004 0.046 1057 Dihedral : 18.947 163.661 2127 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.28 % Favored : 94.28 % Rotamer: Outliers : 6.80 % Allowed : 26.21 % Favored : 66.99 % 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: -0.31 (0.31), residues: 682 helix: 1.48 (0.27), residues: 312 sheet: -1.07 (0.46), residues: 132 loop : -1.98 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 184 TYR 0.014 0.002 TYR B 353 PHE 0.026 0.002 PHE A 139 TRP 0.009 0.001 TRP A 206 HIS 0.006 0.002 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.30 ( 7935) covalent geometry : angle 0.60298 / 0.33 (11081) hydrogen bonds : bond 0.05972 / 4.08 ( 396) hydrogen bonds : angle 4.45275 / 3.29 ( 1126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7949 (mmt90) cc_final: 0.7696 (mmt-90) REVERT: A 53 GLU cc_start: 0.7576 (tt0) cc_final: 0.6001 (tt0) REVERT: A 134 LYS cc_start: 0.7479 (mmtt) cc_final: 0.7212 (mmtt) REVERT: A 136 ASP cc_start: 0.7504 (p0) cc_final: 0.7233 (p0) REVERT: A 180 MET cc_start: 0.6867 (mmt) cc_final: 0.6608 (mmt) REVERT: A 184 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7228 (mtp85) REVERT: A 214 LYS cc_start: 0.8514 (ptpt) cc_final: 0.8217 (ptpt) REVERT: A 263 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7589 (ttm170) REVERT: A 280 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7839 (ttmm) REVERT: A 284 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7710 (ttmt) REVERT: B 57 ASP cc_start: 0.6932 (m-30) cc_final: 0.6667 (m-30) REVERT: B 91 VAL cc_start: 0.7924 (t) cc_final: 0.7698 (p) REVERT: B 139 PHE cc_start: 0.7752 (p90) cc_final: 0.7305 (p90) REVERT: B 198 GLN cc_start: 0.7452 (tm-30) cc_final: 0.7042 (tm-30) REVERT: B 241 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7844 (tmtt) outliers start: 42 outliers final: 33 residues processed: 152 average time/residue: 0.1365 time to fit residues: 25.5722 Evaluate side-chains 166 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 356 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 315 HIS ** 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 = 0.4262 r_free = 0.4262 target = 0.185430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.152852 restraints weight = 11081.880| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.32 r_work: 0.3744 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7935 Z= 0.130 Angle : 0.506 10.940 11081 Z= 0.277 Chirality : 0.038 0.209 1284 Planarity : 0.004 0.044 1057 Dihedral : 18.978 161.155 2127 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.40 % Favored : 95.16 % Rotamer: Outliers : 5.34 % Allowed : 27.67 % Favored : 66.99 % 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: 0.06 (0.32), residues: 682 helix: 1.85 (0.27), residues: 312 sheet: -0.98 (0.46), residues: 132 loop : -1.84 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 184 TYR 0.015 0.001 TYR B 353 PHE 0.026 0.002 PHE B 311 TRP 0.012 0.001 TRP B 342 HIS 0.005 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 7935) covalent geometry : angle 0.50574 / 0.28 (11081) hydrogen bonds : bond 0.05171 / 3.57 ( 396) hydrogen bonds : angle 4.18076 / 3.10 ( 1126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7775 (mmt90) cc_final: 0.7533 (mmt90) REVERT: A 21 LYS cc_start: 0.7333 (ptmt) cc_final: 0.6895 (ttpp) REVERT: A 53 GLU cc_start: 0.7415 (tt0) cc_final: 0.5914 (tt0) REVERT: A 134 LYS cc_start: 0.7397 (mmtt) cc_final: 0.7122 (mmtt) REVERT: A 136 ASP cc_start: 0.7451 (p0) cc_final: 0.7200 (p0) REVERT: A 180 MET cc_start: 0.6821 (mmt) cc_final: 0.6574 (mmt) REVERT: A 184 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7498 (mtm-85) REVERT: A 263 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7518 (ttm170) REVERT: A 280 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7761 (mtmt) REVERT: B 57 ASP cc_start: 0.6805 (m-30) cc_final: 0.6552 (m-30) REVERT: B 91 VAL cc_start: 0.7909 (t) cc_final: 0.7690 (p) REVERT: B 139 PHE cc_start: 0.7710 (p90) cc_final: 0.7254 (p90) REVERT: B 198 GLN cc_start: 0.7395 (tm-30) cc_final: 0.6981 (tm-30) REVERT: B 238 LYS cc_start: 0.7072 (tppt) cc_final: 0.6853 (mtpp) REVERT: B 241 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7723 (tmtt) outliers start: 33 outliers final: 28 residues processed: 147 average time/residue: 0.1380 time to fit residues: 25.1722 Evaluate side-chains 157 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 356 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 42 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4267 r_free = 0.4267 target = 0.185626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153042 restraints weight = 11046.948| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.32 r_work: 0.3755 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7935 Z= 0.138 Angle : 0.507 10.959 11081 Z= 0.278 Chirality : 0.038 0.219 1284 Planarity : 0.003 0.041 1057 Dihedral : 18.897 161.515 2127 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.40 % Favored : 95.16 % Rotamer: Outliers : 5.34 % Allowed : 27.18 % Favored : 67.48 % 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: 0.09 (0.32), residues: 682 helix: 1.89 (0.27), residues: 312 sheet: -0.98 (0.46), residues: 132 loop : -1.83 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 184 TYR 0.016 0.001 TYR B 353 PHE 0.027 0.002 PHE B 311 TRP 0.019 0.001 TRP B 342 HIS 0.006 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 7935) covalent geometry : angle 0.50744 / 0.28 (11081) hydrogen bonds : bond 0.05039 / 3.48 ( 396) hydrogen bonds : angle 4.13223 / 3.06 ( 1126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7766 (mmt90) cc_final: 0.7532 (mmt90) REVERT: A 53 GLU cc_start: 0.7445 (tt0) cc_final: 0.6236 (tp30) REVERT: A 134 LYS cc_start: 0.7411 (mmtt) cc_final: 0.7143 (mmtt) REVERT: A 136 ASP cc_start: 0.7432 (p0) cc_final: 0.7171 (p0) REVERT: A 180 MET cc_start: 0.6795 (mmt) cc_final: 0.6592 (mmt) REVERT: A 184 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7272 (mtp85) REVERT: A 263 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7498 (ttm170) REVERT: A 280 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7816 (ttmm) REVERT: B 57 ASP cc_start: 0.6822 (m-30) cc_final: 0.6578 (m-30) REVERT: B 91 VAL cc_start: 0.7918 (t) cc_final: 0.7699 (p) REVERT: B 139 PHE cc_start: 0.7680 (p90) cc_final: 0.7235 (p90) REVERT: B 198 GLN cc_start: 0.7402 (tm-30) cc_final: 0.7013 (tm-30) REVERT: B 238 LYS cc_start: 0.7088 (tppt) cc_final: 0.6878 (mtpp) REVERT: B 241 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7725 (tmtt) outliers start: 33 outliers final: 29 residues processed: 148 average time/residue: 0.1363 time to fit residues: 24.9893 Evaluate side-chains 158 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 356 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 35 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4277 r_free = 0.4277 target = 0.185506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.153554 restraints weight = 11041.922| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.28 r_work: 0.3761 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7935 Z= 0.134 Angle : 0.500 10.626 11081 Z= 0.275 Chirality : 0.037 0.218 1284 Planarity : 0.004 0.051 1057 Dihedral : 18.868 161.494 2127 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.40 % Favored : 95.16 % Rotamer: Outliers : 4.69 % Allowed : 28.32 % Favored : 66.99 % 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: 0.14 (0.32), residues: 682 helix: 1.92 (0.27), residues: 313 sheet: -0.96 (0.46), residues: 132 loop : -1.80 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG B 184 TYR 0.016 0.001 TYR B 353 PHE 0.025 0.002 PHE B 311 TRP 0.016 0.001 TRP B 342 HIS 0.005 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 7935) covalent geometry : angle 0.49956 / 0.28 (11081) hydrogen bonds : bond 0.04936 / 3.41 ( 396) hydrogen bonds : angle 4.07586 / 3.03 ( 1126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.7755 (mmt90) cc_final: 0.7543 (mmt90) REVERT: A 53 GLU cc_start: 0.7413 (tt0) cc_final: 0.6213 (tp30) REVERT: A 134 LYS cc_start: 0.7417 (mmtt) cc_final: 0.7140 (mmtt) REVERT: A 136 ASP cc_start: 0.7476 (p0) cc_final: 0.7234 (p0) REVERT: A 184 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7246 (mtp85) REVERT: A 214 LYS cc_start: 0.8453 (ptpt) cc_final: 0.8148 (ptpt) REVERT: A 263 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7413 (ttp-110) REVERT: B 57 ASP cc_start: 0.6814 (m-30) cc_final: 0.6575 (m-30) REVERT: B 91 VAL cc_start: 0.7913 (t) cc_final: 0.7694 (p) REVERT: B 139 PHE cc_start: 0.7675 (p90) cc_final: 0.7251 (p90) REVERT: B 198 GLN cc_start: 0.7375 (tm-30) cc_final: 0.6992 (tm-30) REVERT: B 238 LYS cc_start: 0.7087 (tppt) cc_final: 0.6884 (mtpp) REVERT: B 241 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7715 (tmtt) outliers start: 29 outliers final: 27 residues processed: 146 average time/residue: 0.1327 time to fit residues: 24.1274 Evaluate side-chains 159 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 356 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 11 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4284 r_free = 0.4284 target = 0.186052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.153635 restraints weight = 11017.127| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.40 r_work: 0.3751 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7935 Z= 0.121 Angle : 0.519 12.951 11081 Z= 0.282 Chirality : 0.037 0.214 1284 Planarity : 0.004 0.079 1057 Dihedral : 18.837 161.284 2123 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.11 % Favored : 95.45 % Rotamer: Outliers : 4.85 % Allowed : 28.16 % Favored : 66.99 % 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: 0.22 (0.32), residues: 682 helix: 2.00 (0.27), residues: 313 sheet: -0.95 (0.46), residues: 132 loop : -1.76 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG B 184 TYR 0.016 0.001 TYR B 353 PHE 0.027 0.002 PHE B 311 TRP 0.015 0.001 TRP B 342 HIS 0.004 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 7935) covalent geometry : angle 0.51918 / 0.28 (11081) hydrogen bonds : bond 0.04836 / 3.35 ( 396) hydrogen bonds : angle 4.04654 / 3.01 ( 1126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1772.93 seconds wall clock time: 31 minutes 16.95 seconds (1876.95 seconds total)