Starting phenix.real_space_refine on Wed Aug 5 22:42:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10zy_75577/08_2026/10zy_75577.cif Found real_map, /net/cci-nas-00/data/ceres_data/10zy_75577/08_2026/10zy_75577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10zy_75577/08_2026/10zy_75577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10zy_75577/08_2026/10zy_75577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10zy_75577/08_2026/10zy_75577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10zy_75577/08_2026/10zy_75577.map" } resolution = 2.74 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= 1.031 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 133 5.49 5 Mg 3 5.21 5 S 30 5.16 5 C 7035 2.51 5 N 2138 2.21 5 O 2601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11940 Number of models: 1 Model: "" Number of chains: 8 Chain: "1" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2846 Classifications: {'RNA': 133} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 7, 'rna3p_pur': 59, 'rna3p_pyr': 49} Link IDs: {'rna2p': 25, 'rna3p': 107} Chain breaks: 4 Chain: "G" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1263 Classifications: {'peptide': 164} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 155} Chain: "N" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1158 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "R" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3373 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 16, 'TRANS': 414} Chain breaks: 7 Chain: "b" Number of atoms: 1981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1981 Classifications: {'peptide': 243} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 229} Chain breaks: 2 Chain: "i" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 498 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "m" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 818 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "1" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.42, per 1000 atoms: 0.20 Number of scatterers: 11940 At special positions: 0 Unit cell: (109.448, 107.323, 132.825, 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 133 15.00 Mg 3 11.99 O 2601 8.00 N 2138 7.00 C 7035 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: 0.88 Conformation dependent library (CDL) restraints added in 453.8 milliseconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 13 sheets defined 37.8% alpha, 28.4% beta 39 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 83 through 96 removed outlier: 3.807A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 118 Processing helix chain 'G' and resid 121 through 126 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 190 removed outlier: 3.551A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 220 removed outlier: 3.528A pdb=" N ALA G 220 " --> pdb=" O SER G 216 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 16 through 32 removed outlier: 3.538A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 removed outlier: 3.591A pdb=" N ASP N 153 " --> pdb=" O TRP N 150 " (cutoff:3.500A) Proline residue: N 154 - end of helix Processing helix chain 'R' and resid 63 through 67 Processing helix chain 'R' and resid 68 through 74 Processing helix chain 'R' and resid 76 through 80 removed outlier: 3.508A pdb=" N TYR R 79 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 106 removed outlier: 3.938A pdb=" N ASN R 106 " --> pdb=" O PRO R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 485 through 489 Processing helix chain 'R' and resid 509 through 516 Processing helix chain 'R' and resid 516 through 535 Processing helix chain 'b' and resid 3 through 9 Processing helix chain 'b' and resid 42 through 56 Processing helix chain 'b' and resid 72 through 81 removed outlier: 3.778A pdb=" N GLU b 76 " --> pdb=" O GLN b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 145 Processing helix chain 'b' and resid 146 through 161 Processing helix chain 'b' and resid 244 through 271 Processing helix chain 'i' and resid 37 through 49 Processing helix chain 'i' and resid 51 through 65 removed outlier: 3.696A pdb=" N GLY i 65 " --> pdb=" O ILE i 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 78 removed outlier: 4.050A pdb=" N ALA i 69 " --> pdb=" O GLY i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 97 Processing helix chain 'm' and resid 197 through 209 Processing helix chain 'm' and resid 211 through 215 Processing helix chain 'm' and resid 216 through 220 removed outlier: 3.636A pdb=" N GLU m 219 " --> pdb=" O SER m 216 " (cutoff:3.500A) Processing helix chain 'm' and resid 229 through 233 Processing helix chain 'm' and resid 238 through 264 Processing helix chain 'm' and resid 281 through 292 Processing sheet with id=AA1, first strand: chain 'R' and resid 82 through 83 removed outlier: 3.676A pdb=" N LYS R 111 " --> pdb=" O SER R 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AA3, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.430A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLN N 123 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL N 135 " --> pdb=" O VAL N 115 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL N 115 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 2 through 4 removed outlier: 5.416A pdb=" N ILE R 2 " --> pdb=" O THR R 152 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR R 152 " --> pdb=" O ILE R 2 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA R 4 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU R 146 " --> pdb=" O VAL R 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 2 through 4 removed outlier: 5.416A pdb=" N ILE R 2 " --> pdb=" O THR R 152 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR R 152 " --> pdb=" O ILE R 2 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA R 4 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER R 157 " --> pdb=" O MET R 204 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N MET R 204 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU R 159 " --> pdb=" O ASP R 202 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP R 202 " --> pdb=" O LEU R 159 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE R 161 " --> pdb=" O HIS R 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 209 through 217 removed outlier: 4.852A pdb=" N TYR R 217 " --> pdb=" O ALA R 227 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA R 227 " --> pdb=" O TYR R 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 289 through 294 removed outlier: 6.650A pdb=" N VAL R 311 " --> pdb=" O SER R 324 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER R 324 " --> pdb=" O VAL R 311 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU R 313 " --> pdb=" O ALA R 322 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN R 320 " --> pdb=" O ASP R 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 334 through 339 removed outlier: 3.657A pdb=" N GLY R 351 " --> pdb=" O ARG R 355 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG R 355 " --> pdb=" O GLY R 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 381 through 386 removed outlier: 4.481A pdb=" N ASN R 400 " --> pdb=" O THR R 396 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP R 416 " --> pdb=" O SER R 403 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 425 through 430 removed outlier: 3.723A pdb=" N THR R 427 " --> pdb=" O GLY R 441 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA R 442 " --> pdb=" O THR R 447 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR R 447 " --> pdb=" O ALA R 442 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL R 448 " --> pdb=" O SER R 469 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER R 469 " --> pdb=" O VAL R 448 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU R 450 " --> pdb=" O VAL R 467 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 477 through 482 Processing sheet with id=AB3, first strand: chain 'b' and resid 59 through 61 removed outlier: 4.884A pdb=" N LEU b 97 " --> pdb=" O ILE b 114 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR b 109 " --> pdb=" O ILE b 226 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE b 226 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS b 111 " --> pdb=" O ILE b 224 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU b 117 " --> pdb=" O ARG b 218 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG b 218 " --> pdb=" O LEU b 117 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE b 224 " --> pdb=" O GLU b 238 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU b 238 " --> pdb=" O ILE b 224 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE b 226 " --> pdb=" O ILE b 236 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 59 through 61 removed outlier: 4.884A pdb=" N LEU b 97 " --> pdb=" O ILE b 114 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR b 109 " --> pdb=" O ILE b 226 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE b 226 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS b 111 " --> pdb=" O ILE b 224 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU b 117 " --> pdb=" O ARG b 218 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG b 218 " --> pdb=" O LEU b 117 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL b 213 " --> pdb=" O SER b 194 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER b 194 " --> pdb=" O VAL b 213 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE b 215 " --> pdb=" O GLU b 192 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLU b 192 " --> pdb=" O ILE b 215 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR b 190 " --> pdb=" O PRO b 217 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL b 136 " --> pdb=" O MET b 177 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE b 179 " --> pdb=" O VAL b 136 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER b 138 " --> pdb=" O PHE b 179 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE b 181 " --> pdb=" O SER b 138 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU b 137 " --> pdb=" O VAL m 223 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.21 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: 2292 1.33 - 1.45: 3566 1.45 - 1.57: 6280 1.57 - 1.69: 261 1.69 - 1.81: 52 Bond restraints: 12451 Sorted by residual: bond pdb=" C2 U 1 149 " pdb=" N3 U 1 149 " ideal model delta sigma weight residual 1.373 1.360 0.013 7.00e-03 2.04e+04 3.38e+00 bond pdb=" N MET R 1 " pdb=" CA MET R 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" N7 G 1 267 " pdb=" C5 G 1 267 " ideal model delta sigma weight residual 1.388 1.379 0.009 6.00e-03 2.78e+04 2.10e+00 bond pdb=" N9 A 1 268 " pdb=" C4 A 1 268 " ideal model delta sigma weight residual 1.374 1.365 0.009 6.00e-03 2.78e+04 2.10e+00 bond pdb=" N7 A 1 295 " pdb=" C5 A 1 295 " ideal model delta sigma weight residual 1.388 1.380 0.008 6.00e-03 2.78e+04 2.00e+00 ... (remaining 12446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 16464 1.32 - 2.64: 863 2.64 - 3.97: 97 3.97 - 5.29: 15 5.29 - 6.61: 5 Bond angle restraints: 17444 Sorted by residual: angle pdb=" O5' C 1 69 " pdb=" C5' C 1 69 " pdb=" C4' C 1 69 " ideal model delta sigma weight residual 109.40 112.79 -3.39 8.00e-01 1.56e+00 1.79e+01 angle pdb=" O4' A 1 65 " pdb=" C1' A 1 65 " pdb=" N9 A 1 65 " ideal model delta sigma weight residual 108.20 111.51 -3.31 8.00e-01 1.56e+00 1.72e+01 angle pdb=" O5' G 1 143 " pdb=" C5' G 1 143 " pdb=" C4' G 1 143 " ideal model delta sigma weight residual 109.40 112.66 -3.26 8.00e-01 1.56e+00 1.66e+01 angle pdb=" O5' A 1 122 " pdb=" C5' A 1 122 " pdb=" C4' A 1 122 " ideal model delta sigma weight residual 109.40 112.66 -3.26 8.00e-01 1.56e+00 1.66e+01 angle pdb=" O5' C 1 293 " pdb=" C5' C 1 293 " pdb=" C4' C 1 293 " ideal model delta sigma weight residual 109.40 112.51 -3.11 8.00e-01 1.56e+00 1.51e+01 ... (remaining 17439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.33: 6933 20.33 - 40.67: 447 40.67 - 61.00: 177 61.00 - 81.34: 97 81.34 - 101.67: 3 Dihedral angle restraints: 7657 sinusoidal: 4335 harmonic: 3322 Sorted by residual: dihedral pdb=" CA LYS R 67 " pdb=" C LYS R 67 " pdb=" N ASP R 68 " pdb=" CA ASP R 68 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LYS b 170 " pdb=" C LYS b 170 " pdb=" N PRO b 171 " pdb=" CA PRO b 171 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ARG N 67 " pdb=" C ARG N 67 " pdb=" N ARG N 68 " pdb=" CA ARG N 68 " ideal model delta harmonic sigma weight residual -180.00 -160.04 -19.96 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 7654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1311 0.035 - 0.070: 421 0.070 - 0.106: 218 0.106 - 0.141: 81 0.141 - 0.176: 9 Chirality restraints: 2040 Sorted by residual: chirality pdb=" C1' A 1 323 " pdb=" O4' A 1 323 " pdb=" C2' A 1 323 " pdb=" N9 A 1 323 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA ARG b 218 " pdb=" N ARG b 218 " pdb=" C ARG b 218 " pdb=" CB ARG b 218 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA PRO b 171 " pdb=" N PRO b 171 " pdb=" C PRO b 171 " pdb=" CB PRO b 171 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 2037 not shown) Planarity restraints: 1734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 84 " 0.205 9.50e-02 1.11e+02 9.22e-02 5.62e+00 pdb=" NE ARG G 84 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG G 84 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG G 84 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 84 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 296 " 0.031 2.00e-02 2.50e+03 1.41e-02 5.43e+00 pdb=" N9 A 1 296 " -0.032 2.00e-02 2.50e+03 pdb=" C8 A 1 296 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A 1 296 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A 1 296 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 1 296 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A 1 296 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A 1 296 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A 1 296 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A 1 296 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A 1 296 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 65 " -0.031 2.00e-02 2.50e+03 1.36e-02 5.06e+00 pdb=" N9 A 1 65 " 0.029 2.00e-02 2.50e+03 pdb=" C8 A 1 65 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A 1 65 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 1 65 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 1 65 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 1 65 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A 1 65 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 1 65 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 1 65 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A 1 65 " 0.008 2.00e-02 2.50e+03 ... (remaining 1731 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 76 2.56 - 3.14: 8886 3.14 - 3.73: 19506 3.73 - 4.31: 29087 4.31 - 4.90: 44701 Nonbonded interactions: 102256 Sorted by model distance: nonbonded pdb=" OG SER R 291 " pdb=" OG1 THR R 305 " model vdw 1.969 3.040 nonbonded pdb=" OP2 A 1 317 " pdb="MG MG 13402 " model vdw 2.103 2.170 nonbonded pdb=" OP2 A 1 307 " pdb=" NZ LYS b 235 " model vdw 2.170 3.120 nonbonded pdb=" OD2 ASP R 75 " pdb=" NZ LYS R 77 " model vdw 2.193 3.120 nonbonded pdb=" OD2 ASP R 165 " pdb=" NH1 ARG R 193 " model vdw 2.232 3.120 ... (remaining 102251 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: 1.820 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.720 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: 0.010 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12451 Z= 0.212 Angle : 0.636 6.608 17444 Z= 0.458 Chirality : 0.048 0.176 2040 Planarity : 0.005 0.092 1734 Dihedral : 16.724 101.675 5495 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.23 (0.26), residues: 1100 helix: 1.85 (0.28), residues: 360 sheet: 0.50 (0.30), residues: 283 loop : 0.33 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 84 TYR 0.013 0.001 TYR i 53 PHE 0.013 0.002 PHE b 112 TRP 0.010 0.002 TRP R 416 HIS 0.005 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.21 (12451) covalent geometry : angle 0.63580 / 0.46 (17444) hydrogen bonds : bond 0.10972 / 12.25 ( 515) hydrogen bonds : angle 5.36453 / 6.58 ( 1382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: N 124 ASP cc_start: 0.7816 (p0) cc_final: 0.7495 (p0) REVERT: b 84 ASN cc_start: 0.8245 (p0) cc_final: 0.7967 (p0) outliers start: 0 outliers final: 1 residues processed: 184 average time/residue: 0.7680 time to fit residues: 150.4019 Evaluate side-chains 154 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 363 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 117 ASN R 69 GLN R 524 GLN m 197 ASN m 209 GLN m 284 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125201 restraints weight = 12018.342| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.80 r_work: 0.3094 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12451 Z= 0.134 Angle : 0.514 6.416 17444 Z= 0.290 Chirality : 0.040 0.174 2040 Planarity : 0.004 0.049 1734 Dihedral : 17.870 97.916 3233 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.42 % Allowed : 9.72 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.34 (0.25), residues: 1100 helix: 2.21 (0.27), residues: 365 sheet: 0.61 (0.30), residues: 273 loop : 0.06 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 84 TYR 0.010 0.001 TYR m 247 PHE 0.011 0.002 PHE m 217 TRP 0.012 0.002 TRP R 416 HIS 0.004 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (12451) covalent geometry : angle 0.51387 / 0.29 (17444) hydrogen bonds : bond 0.04865 / 5.26 ( 515) hydrogen bonds : angle 4.41792 / 5.37 ( 1382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 543 LYS cc_start: 0.7501 (ttmt) cc_final: 0.6957 (tmtt) REVERT: b 32 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7594 (mtm110) REVERT: b 183 ASP cc_start: 0.8263 (t0) cc_final: 0.7974 (t0) REVERT: i 38 LYS cc_start: 0.8160 (mptt) cc_final: 0.7882 (ptpp) outliers start: 14 outliers final: 5 residues processed: 161 average time/residue: 0.7251 time to fit residues: 124.9812 Evaluate side-chains 155 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain R residue 96 LYS Chi-restraints excluded: chain R residue 497 VAL Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 211 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... m 197 ASN m 209 GLN m 232 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.154121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125921 restraints weight = 12019.065| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.60 r_work: 0.3064 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12451 Z= 0.168 Angle : 0.527 6.439 17444 Z= 0.294 Chirality : 0.042 0.196 2040 Planarity : 0.005 0.052 1734 Dihedral : 17.864 96.909 3231 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.73 % Allowed : 9.92 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.36 (0.25), residues: 1100 helix: 2.23 (0.27), residues: 365 sheet: 0.66 (0.30), residues: 285 loop : 0.03 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 189 TYR 0.010 0.001 TYR R 544 PHE 0.014 0.002 PHE b 112 TRP 0.013 0.002 TRP R 416 HIS 0.007 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (12451) covalent geometry : angle 0.52696 / 0.29 (17444) hydrogen bonds : bond 0.05136 / 5.50 ( 515) hydrogen bonds : angle 4.24306 / 5.23 ( 1382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 521 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: R 543 LYS cc_start: 0.7438 (ttmt) cc_final: 0.6866 (tmtt) REVERT: b 32 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7491 (mtm110) REVERT: b 183 ASP cc_start: 0.8499 (t0) cc_final: 0.8099 (t0) REVERT: i 38 LYS cc_start: 0.8136 (mptt) cc_final: 0.7930 (ptpp) REVERT: m 236 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8052 (mp) REVERT: m 291 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6788 (ttpt) outliers start: 27 outliers final: 11 residues processed: 166 average time/residue: 0.7378 time to fit residues: 131.0395 Evaluate side-chains 165 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain R residue 96 LYS Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 497 VAL Chi-restraints excluded: chain R residue 521 GLU Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 121 ASP Chi-restraints excluded: chain b residue 211 SER Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain m residue 236 ILE Chi-restraints excluded: chain m residue 273 ASP Chi-restraints excluded: chain m residue 291 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 509 ASN b 85 ASN m 197 ASN m 209 GLN m 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126705 restraints weight = 12060.357| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.65 r_work: 0.3082 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12451 Z= 0.128 Angle : 0.477 6.268 17444 Z= 0.271 Chirality : 0.039 0.169 2040 Planarity : 0.004 0.036 1734 Dihedral : 17.791 97.344 3231 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.13 % Allowed : 12.04 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.38 (0.25), residues: 1100 helix: 2.26 (0.27), residues: 368 sheet: 0.73 (0.30), residues: 285 loop : -0.04 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 189 TYR 0.009 0.001 TYR b 81 PHE 0.014 0.002 PHE m 217 TRP 0.011 0.001 TRP R 416 HIS 0.005 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (12451) covalent geometry : angle 0.47658 / 0.27 (17444) hydrogen bonds : bond 0.04677 / 4.99 ( 515) hydrogen bonds : angle 4.11482 / 5.03 ( 1382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 341 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8368 (mtp) REVERT: R 521 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7633 (mm-30) REVERT: R 543 LYS cc_start: 0.7313 (ttmt) cc_final: 0.6822 (tmtt) REVERT: b 32 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7447 (mtm110) REVERT: b 183 ASP cc_start: 0.8469 (t0) cc_final: 0.8101 (t0) REVERT: m 236 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8044 (mp) REVERT: m 291 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6805 (ttpt) outliers start: 21 outliers final: 12 residues processed: 165 average time/residue: 0.7009 time to fit residues: 124.0068 Evaluate side-chains 168 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain R residue 96 LYS Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 341 MET Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 497 VAL Chi-restraints excluded: chain R residue 521 GLU Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 121 ASP Chi-restraints excluded: chain b residue 211 SER Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain m residue 236 ILE Chi-restraints excluded: chain m residue 273 ASP Chi-restraints excluded: chain m residue 291 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 123 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 127 ASN b 255 GLN m 197 ASN m 209 GLN m 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129505 restraints weight = 12005.196| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.47 r_work: 0.3100 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12451 Z= 0.118 Angle : 0.464 5.574 17444 Z= 0.264 Chirality : 0.039 0.169 2040 Planarity : 0.004 0.036 1734 Dihedral : 17.730 97.669 3231 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.02 % Allowed : 12.75 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.43 (0.25), residues: 1100 helix: 2.32 (0.27), residues: 367 sheet: 0.75 (0.30), residues: 285 loop : -0.02 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG i 68 TYR 0.009 0.001 TYR i 53 PHE 0.014 0.001 PHE m 217 TRP 0.012 0.001 TRP R 416 HIS 0.005 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (12451) covalent geometry : angle 0.46449 / 0.26 (17444) hydrogen bonds : bond 0.04498 / 4.81 ( 515) hydrogen bonds : angle 3.99338 / 4.90 ( 1382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 214 LEU cc_start: 0.8465 (mt) cc_final: 0.8250 (mt) REVERT: R 341 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8429 (mtp) REVERT: R 363 ILE cc_start: 0.9042 (mp) cc_final: 0.8770 (mp) REVERT: R 543 LYS cc_start: 0.7221 (ttmt) cc_final: 0.6691 (tmtt) REVERT: b 32 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7471 (mtm110) REVERT: b 183 ASP cc_start: 0.8494 (t0) cc_final: 0.8168 (t0) REVERT: m 236 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8035 (mp) outliers start: 20 outliers final: 12 residues processed: 156 average time/residue: 0.6576 time to fit residues: 110.1481 Evaluate side-chains 157 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 341 MET Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 497 VAL Chi-restraints excluded: chain R residue 521 GLU Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 121 ASP Chi-restraints excluded: chain b residue 211 SER Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain m residue 236 ILE Chi-restraints excluded: chain m residue 273 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 95 ASN b 75 ASN m 197 ASN m 209 GLN m 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125811 restraints weight = 12036.703| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.57 r_work: 0.3057 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12451 Z= 0.174 Angle : 0.521 6.515 17444 Z= 0.290 Chirality : 0.041 0.199 2040 Planarity : 0.004 0.044 1734 Dihedral : 17.771 96.987 3231 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.53 % Allowed : 13.46 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.37 (0.25), residues: 1100 helix: 2.28 (0.27), residues: 365 sheet: 0.75 (0.30), residues: 285 loop : -0.08 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG i 68 TYR 0.010 0.001 TYR b 237 PHE 0.016 0.002 PHE b 112 TRP 0.013 0.002 TRP R 416 HIS 0.008 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (12451) covalent geometry : angle 0.52103 / 0.29 (17444) hydrogen bonds : bond 0.05018 / 5.35 ( 515) hydrogen bonds : angle 4.13296 / 5.11 ( 1382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 363 ILE cc_start: 0.9072 (mp) cc_final: 0.8791 (mp) REVERT: b 32 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7408 (mtm110) REVERT: b 183 ASP cc_start: 0.8618 (t0) cc_final: 0.8305 (t0) REVERT: m 236 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8096 (mp) outliers start: 25 outliers final: 14 residues processed: 154 average time/residue: 0.6188 time to fit residues: 102.6314 Evaluate side-chains 159 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 497 VAL Chi-restraints excluded: chain R residue 521 GLU Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 121 ASP Chi-restraints excluded: chain b residue 211 SER Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain m residue 236 ILE Chi-restraints excluded: chain m residue 241 GLU Chi-restraints excluded: chain m residue 273 ASP Chi-restraints excluded: chain m residue 282 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 95 ASN R 127 ASN m 197 ASN m 209 GLN m 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124337 restraints weight = 12063.962| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.80 r_work: 0.3082 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12451 Z= 0.123 Angle : 0.466 5.721 17444 Z= 0.265 Chirality : 0.039 0.165 2040 Planarity : 0.004 0.040 1734 Dihedral : 17.730 97.538 3231 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.23 % Allowed : 14.27 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.42 (0.26), residues: 1100 helix: 2.34 (0.27), residues: 368 sheet: 0.75 (0.30), residues: 295 loop : -0.07 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG i 68 TYR 0.010 0.001 TYR i 53 PHE 0.014 0.001 PHE m 217 TRP 0.012 0.001 TRP R 416 HIS 0.005 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (12451) covalent geometry : angle 0.46623 / 0.26 (17444) hydrogen bonds : bond 0.04560 / 4.86 ( 515) hydrogen bonds : angle 4.01855 / 4.94 ( 1382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 363 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8760 (mp) REVERT: b 32 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7379 (mtm110) REVERT: b 183 ASP cc_start: 0.8578 (t0) cc_final: 0.8299 (t0) REVERT: b 235 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7529 (ttmm) REVERT: m 236 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8051 (mp) outliers start: 22 outliers final: 14 residues processed: 158 average time/residue: 0.5885 time to fit residues: 99.8921 Evaluate side-chains 164 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain R residue 96 LYS Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 497 VAL Chi-restraints excluded: chain R residue 521 GLU Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 121 ASP Chi-restraints excluded: chain b residue 211 SER Chi-restraints excluded: chain b residue 235 LYS Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain m residue 236 ILE Chi-restraints excluded: chain m residue 273 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 66 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 95 ASN R 127 ASN m 197 ASN m 209 GLN m 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124549 restraints weight = 12015.983| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.76 r_work: 0.3083 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12451 Z= 0.127 Angle : 0.473 5.763 17444 Z= 0.268 Chirality : 0.039 0.177 2040 Planarity : 0.004 0.041 1734 Dihedral : 17.708 97.482 3231 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.94 % Allowed : 14.07 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.44 (0.25), residues: 1100 helix: 2.35 (0.27), residues: 367 sheet: 0.77 (0.30), residues: 295 loop : -0.06 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG i 68 TYR 0.010 0.001 TYR b 81 PHE 0.015 0.002 PHE R 251 TRP 0.012 0.001 TRP R 416 HIS 0.006 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (12451) covalent geometry : angle 0.47326 / 0.27 (17444) hydrogen bonds : bond 0.04572 / 4.88 ( 515) hydrogen bonds : angle 3.98140 / 4.91 ( 1382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.8392 (ttm) cc_final: 0.8098 (ttp) REVERT: b 32 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7379 (mtm110) REVERT: b 183 ASP cc_start: 0.8584 (t0) cc_final: 0.8335 (t0) REVERT: b 235 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7523 (ttmm) REVERT: m 236 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8056 (mp) outliers start: 29 outliers final: 18 residues processed: 157 average time/residue: 0.6250 time to fit residues: 105.4529 Evaluate side-chains 168 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 497 VAL Chi-restraints excluded: chain R residue 521 GLU Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 121 ASP Chi-restraints excluded: chain b residue 211 SER Chi-restraints excluded: chain b residue 235 LYS Chi-restraints excluded: chain b residue 261 LYS Chi-restraints excluded: chain i residue 38 LYS Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain m residue 236 ILE Chi-restraints excluded: chain m residue 241 GLU Chi-restraints excluded: chain m residue 273 ASP Chi-restraints excluded: chain m residue 282 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 95 ASN R 127 ASN R 368 GLN m 197 ASN m 209 GLN m 232 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.155737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124886 restraints weight = 11939.046| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.79 r_work: 0.3092 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12451 Z= 0.120 Angle : 0.464 5.380 17444 Z= 0.263 Chirality : 0.039 0.166 2040 Planarity : 0.004 0.039 1734 Dihedral : 17.694 97.510 3231 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.23 % Allowed : 14.78 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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 (0.26), residues: 1100 helix: 2.39 (0.27), residues: 368 sheet: 0.78 (0.30), residues: 295 loop : -0.05 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG i 68 TYR 0.010 0.001 TYR i 53 PHE 0.014 0.001 PHE m 217 TRP 0.012 0.001 TRP R 416 HIS 0.005 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (12451) covalent geometry : angle 0.46380 / 0.26 (17444) hydrogen bonds : bond 0.04460 / 4.76 ( 515) hydrogen bonds : angle 3.95395 / 4.87 ( 1382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.8436 (ttm) cc_final: 0.8142 (ttp) REVERT: b 32 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7359 (mtm110) REVERT: b 183 ASP cc_start: 0.8581 (t0) cc_final: 0.8344 (t0) REVERT: b 235 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7509 (ttmm) REVERT: m 236 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8019 (mp) outliers start: 22 outliers final: 16 residues processed: 157 average time/residue: 0.5985 time to fit residues: 101.0993 Evaluate side-chains 167 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 96 ARG Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 383 THR Chi-restraints excluded: chain R residue 497 VAL Chi-restraints excluded: chain R residue 521 GLU Chi-restraints excluded: chain b residue 32 ARG Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 121 ASP Chi-restraints excluded: chain b residue 211 SER Chi-restraints excluded: chain b residue 235 LYS Chi-restraints excluded: chain b residue 261 LYS Chi-restraints excluded: chain i residue 38 LYS Chi-restraints excluded: chain i residue 47 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain m residue 236 ILE Chi-restraints excluded: chain m residue 241 GLU Chi-restraints excluded: chain m residue 273 ASP Chi-restraints excluded: chain m residue 282 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 9.9990 chunk 90 optimal weight: 0.0670 chunk 13 optimal weight: 0.0870 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 97 optimal weight: 0.0870 chunk 74 optimal weight: 0.0370 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 overall best weight: 0.2152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 95 ASN R 127 ASN R 368 GLN m 197 ASN m 209 GLN m 221 GLN m 232 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.159147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129773 restraints weight = 12202.408| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.71 r_work: 0.3142 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12451 Z= 0.090 Angle : 0.436 5.031 17444 Z= 0.250 Chirality : 0.037 0.171 2040 Planarity : 0.003 0.035 1734 Dihedral : 17.643 98.293 3231 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.42 % Allowed : 15.89 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.55 (0.26), residues: 1100 helix: 2.47 (0.27), residues: 367 sheet: 0.79 (0.30), residues: 295 loop : 0.01 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG i 68 TYR 0.012 0.001 TYR i 53 PHE 0.013 0.001 PHE m 217 TRP 0.014 0.001 TRP R 416 HIS 0.002 0.001 HIS R 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.09 (12451) covalent geometry : angle 0.43560 / 0.25 (17444) hydrogen bonds : bond 0.04037 / 4.28 ( 515) hydrogen bonds : angle 3.77153 / 4.65 ( 1382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 1 MET cc_start: 0.8349 (ttm) cc_final: 0.8064 (ttp) REVERT: b 174 ASP cc_start: 0.7619 (t0) cc_final: 0.7288 (t0) REVERT: m 236 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8006 (mp) outliers start: 14 outliers final: 10 residues processed: 151 average time/residue: 0.5943 time to fit residues: 96.6441 Evaluate side-chains 157 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 104 GLU Chi-restraints excluded: chain R residue 155 ASP Chi-restraints excluded: chain R residue 497 VAL Chi-restraints excluded: chain R residue 521 GLU Chi-restraints excluded: chain b residue 66 ASP Chi-restraints excluded: chain b residue 121 ASP Chi-restraints excluded: chain b residue 211 SER Chi-restraints excluded: chain b residue 261 LYS Chi-restraints excluded: chain i residue 38 LYS Chi-restraints excluded: chain m residue 236 ILE Chi-restraints excluded: chain m residue 282 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 0.0570 chunk 4 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 95 ASN R 127 ASN R 368 GLN ** R 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.155421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124291 restraints weight = 12018.117| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.79 r_work: 0.3080 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12451 Z= 0.147 Angle : 0.498 7.351 17444 Z= 0.279 Chirality : 0.040 0.180 2040 Planarity : 0.004 0.037 1734 Dihedral : 17.667 97.518 3231 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.92 % Allowed : 15.49 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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 (0.26), residues: 1100 helix: 2.36 (0.27), residues: 369 sheet: 0.85 (0.30), residues: 295 loop : -0.03 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG i 68 TYR 0.011 0.001 TYR b 237 PHE 0.015 0.002 PHE b 112 TRP 0.010 0.002 TRP R 416 HIS 0.007 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (12451) covalent geometry : angle 0.49832 / 0.28 (17444) hydrogen bonds : bond 0.04604 / 4.92 ( 515) hydrogen bonds : angle 3.91927 / 4.85 ( 1382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4401.16 seconds wall clock time: 75 minutes 40.15 seconds (4540.15 seconds total)