Starting phenix.real_space_refine on Thu Mar 5 01:10:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w57_32316/03_2026/7w57_32316.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w57_32316/03_2026/7w57_32316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w57_32316/03_2026/7w57_32316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w57_32316/03_2026/7w57_32316.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w57_32316/03_2026/7w57_32316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w57_32316/03_2026/7w57_32316.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 5859 2.51 5 N 1574 2.21 5 O 1682 1.98 5 H 9072 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18242 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 3752 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 5074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5074 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 201 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 2, 'TRANS': 9} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3502 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 831 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "R" Number of atoms: 4882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 4882 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 14, 'TRANS': 282} Chain breaks: 1 Time building chain proxies: 3.22, per 1000 atoms: 0.18 Number of scatterers: 18242 At special positions: 0 Unit cell: (111.24, 130.68, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 O 1682 8.00 N 1574 7.00 C 5859 6.00 H 9072 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 637.9 milliseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 40.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.652A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.124A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.963A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 11 through 31 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.767A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.583A pdb=" N ILE G 24 " --> pdb=" O MET G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 44 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 44 through 73 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 73 through 78 Processing helix chain 'R' and resid 81 through 108 Proline residue: R 100 - end of helix removed outlier: 3.569A pdb=" N TRP R 107 " --> pdb=" O VAL R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 150 Processing helix chain 'R' and resid 150 through 158 removed outlier: 3.609A pdb=" N LYS R 155 " --> pdb=" O PRO R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 184 removed outlier: 3.542A pdb=" N LEU R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Proline residue: R 180 - end of helix Processing helix chain 'R' and resid 209 through 225 removed outlier: 3.685A pdb=" N PHE R 215 " --> pdb=" O TRP R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 245 Processing helix chain 'R' and resid 258 through 294 Proline residue: R 283 - end of helix removed outlier: 3.588A pdb=" N ARG R 288 " --> pdb=" O PHE R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 328 removed outlier: 3.581A pdb=" N SER R 320 " --> pdb=" O PHE R 316 " (cutoff:3.500A) Proline residue: R 324 - end of helix Processing helix chain 'R' and resid 331 through 345 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.212A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.889A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.593A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.780A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 158 removed outlier: 6.349A pdb=" N GLN B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.728A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.636A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.636A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.975A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.975A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 5.834A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 185 through 189 484 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9045 1.02 - 1.22: 29 1.22 - 1.41: 3941 1.41 - 1.61: 5353 1.61 - 1.81: 81 Bond restraints: 18449 Sorted by residual: bond pdb=" SG CYS R 204 " pdb=" HG CYS R 204 " ideal model delta sigma weight residual 1.200 1.343 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" SG CYS R 119 " pdb=" HG CYS R 119 " ideal model delta sigma weight residual 1.200 1.341 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" ND2 ASN B 298 " pdb="HD21 ASN B 298 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN B 298 " pdb="HD22 ASN B 298 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C ARG E 191 " pdb=" O ARG E 191 " ideal model delta sigma weight residual 1.234 1.164 0.070 1.19e-02 7.06e+03 3.49e+01 ... (remaining 18444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 32932 1.94 - 3.87: 214 3.87 - 5.81: 31 5.81 - 7.74: 4 7.74 - 9.68: 2 Bond angle restraints: 33183 Sorted by residual: angle pdb=" N ASP B 296 " pdb=" CA ASP B 296 " pdb=" C ASP B 296 " ideal model delta sigma weight residual 110.50 100.82 9.68 1.41e+00 5.03e-01 4.71e+01 angle pdb=" N ARG E 191 " pdb=" CA ARG E 191 " pdb=" C ARG E 191 " ideal model delta sigma weight residual 108.42 99.60 8.82 1.54e+00 4.22e-01 3.28e+01 angle pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " ideal model delta sigma weight residual 115.38 123.02 -7.64 1.40e+00 5.10e-01 2.97e+01 angle pdb=" N ASP B 295 " pdb=" CA ASP B 295 " pdb=" C ASP B 295 " ideal model delta sigma weight residual 111.71 105.78 5.93 1.15e+00 7.56e-01 2.66e+01 angle pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" O ARG E 191 " ideal model delta sigma weight residual 121.10 116.25 4.85 1.10e+00 8.26e-01 1.94e+01 ... (remaining 33178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8085 17.91 - 35.82: 439 35.82 - 53.72: 125 53.72 - 71.63: 75 71.63 - 89.54: 8 Dihedral angle restraints: 8732 sinusoidal: 4656 harmonic: 4076 Sorted by residual: dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 204 " pdb=" CB CYS R 204 " ideal model delta sinusoidal sigma weight residual 93.00 177.82 -84.82 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CA GLY B 315 " pdb=" C GLY B 315 " pdb=" N HIS B 316 " pdb=" CA HIS B 316 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA LYS B 83 " pdb=" C LYS B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 8729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1216 0.056 - 0.111: 176 0.111 - 0.167: 26 0.167 - 0.222: 1 0.222 - 0.277: 2 Chirality restraints: 1421 Sorted by residual: chirality pdb=" CB VAL B 117 " pdb=" CA VAL B 117 " pdb=" CG1 VAL B 117 " pdb=" CG2 VAL B 117 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ASP B 296 " pdb=" N ASP B 296 " pdb=" C ASP B 296 " pdb=" CB ASP B 296 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE R 187 " pdb=" N ILE R 187 " pdb=" C ILE R 187 " pdb=" CB ILE R 187 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 1418 not shown) Planarity restraints: 2724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 298 " -0.115 2.00e-02 2.50e+03 1.14e-01 1.95e+02 pdb=" CG ASN B 298 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN B 298 " 0.111 2.00e-02 2.50e+03 pdb=" ND2 ASN B 298 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 298 " 0.161 2.00e-02 2.50e+03 pdb="HD22 ASN B 298 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 274 " -0.011 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" N ILE B 275 " 0.035 2.00e-02 2.50e+03 pdb=" CA ILE B 275 " -0.009 2.00e-02 2.50e+03 pdb=" H ILE B 275 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 222 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C PHE R 222 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE R 222 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU R 223 " -0.011 2.00e-02 2.50e+03 ... (remaining 2721 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 673 2.16 - 2.77: 35380 2.77 - 3.38: 52521 3.38 - 3.99: 68488 3.99 - 4.60: 107225 Nonbonded interactions: 264287 Sorted by model distance: nonbonded pdb="HH11 ARG B 101 " pdb=" OE2 GLU B 143 " model vdw 1.548 2.450 nonbonded pdb=" HG1 THR B 279 " pdb=" O VAL B 320 " model vdw 1.550 2.450 nonbonded pdb=" OE1 GLU B 135 " pdb=" H GLU B 135 " model vdw 1.554 2.450 nonbonded pdb=" H PHE B 240 " pdb=" O ALA B 245 " model vdw 1.556 2.450 nonbonded pdb=" OD2 ASP B 259 " pdb=" H ALA B 262 " model vdw 1.568 2.450 ... (remaining 264282 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.830 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 0.070 9379 Z= 0.192 Angle : 0.579 9.677 12709 Z= 0.351 Chirality : 0.042 0.277 1421 Planarity : 0.003 0.029 1616 Dihedral : 11.438 89.541 3378 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.20 % Allowed : 3.99 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.67 (0.24), residues: 1140 helix: 1.04 (0.24), residues: 405 sheet: 0.11 (0.31), residues: 283 loop : 0.33 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 191 TYR 0.015 0.001 TYR E 190 PHE 0.014 0.001 PHE R 338 TRP 0.010 0.001 TRP B 104 HIS 0.006 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9377) covalent geometry : angle 0.57800 (12705) SS BOND : bond 0.00397 ( 2) SS BOND : angle 1.97473 ( 4) hydrogen bonds : bond 0.16111 ( 480) hydrogen bonds : angle 6.41480 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 236 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8178 (mp0) cc_final: 0.7933 (mp0) REVERT: B 328 ASP cc_start: 0.8186 (p0) cc_final: 0.7849 (p0) REVERT: C 0 ARG cc_start: 0.7962 (mtt180) cc_final: 0.5185 (pmt170) REVERT: R 108 ARG cc_start: 0.7207 (mtp-110) cc_final: 0.6856 (tpt90) REVERT: R 227 LEU cc_start: 0.8638 (tp) cc_final: 0.8356 (mt) REVERT: R 306 ASN cc_start: 0.8139 (m-40) cc_final: 0.7910 (m-40) outliers start: 2 outliers final: 1 residues processed: 234 average time/residue: 0.2956 time to fit residues: 88.5868 Evaluate side-chains 174 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 225 GLN B 273 ASN E 38 GLN E 179 GLN E 183 GLN R 267 ASN R 339 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.143633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109787 restraints weight = 33322.593| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.26 r_work: 0.2922 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9379 Z= 0.145 Angle : 0.530 4.835 12709 Z= 0.291 Chirality : 0.041 0.160 1421 Planarity : 0.004 0.039 1616 Dihedral : 5.161 55.187 1266 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.70 % Allowed : 7.38 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.80 (0.24), residues: 1140 helix: 1.47 (0.25), residues: 410 sheet: -0.06 (0.30), residues: 282 loop : 0.22 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 332 TYR 0.016 0.001 TYR E 190 PHE 0.014 0.001 PHE R 338 TRP 0.015 0.001 TRP B 87 HIS 0.003 0.001 HIS R 73 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9377) covalent geometry : angle 0.52968 (12705) SS BOND : bond 0.00547 ( 2) SS BOND : angle 0.63955 ( 4) hydrogen bonds : bond 0.04780 ( 480) hydrogen bonds : angle 5.33315 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 179 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8662 (ttmm) cc_final: 0.8393 (mtpp) REVERT: B 217 ASP cc_start: 0.8452 (t70) cc_final: 0.8216 (t0) REVERT: C 0 ARG cc_start: 0.7912 (mtt180) cc_final: 0.5166 (pmt170) REVERT: R 45 PHE cc_start: 0.7561 (t80) cc_final: 0.7008 (t80) REVERT: R 108 ARG cc_start: 0.7540 (mtp-110) cc_final: 0.6646 (tpt90) REVERT: R 127 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8046 (mm-30) REVERT: R 211 TRP cc_start: 0.7085 (t60) cc_final: 0.6795 (t60) outliers start: 7 outliers final: 6 residues processed: 184 average time/residue: 0.2828 time to fit residues: 67.4650 Evaluate side-chains 166 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain R residue 230 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 66 optimal weight: 0.0000 chunk 86 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 225 GLN B 273 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110866 restraints weight = 33464.421| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.25 r_work: 0.2926 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9379 Z= 0.143 Angle : 0.510 5.292 12709 Z= 0.276 Chirality : 0.040 0.148 1421 Planarity : 0.004 0.044 1616 Dihedral : 4.975 55.833 1266 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.20 % Allowed : 8.37 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.87 (0.25), residues: 1140 helix: 1.73 (0.25), residues: 410 sheet: -0.19 (0.30), residues: 283 loop : 0.16 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 332 TYR 0.018 0.001 TYR E 190 PHE 0.011 0.001 PHE R 338 TRP 0.015 0.001 TRP B 87 HIS 0.003 0.001 HIS R 73 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9377) covalent geometry : angle 0.50950 (12705) SS BOND : bond 0.00275 ( 2) SS BOND : angle 0.56094 ( 4) hydrogen bonds : bond 0.04357 ( 480) hydrogen bonds : angle 5.09917 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8403 (mtpp) REVERT: B 239 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8459 (m-80) REVERT: C 0 ARG cc_start: 0.7888 (mtt180) cc_final: 0.5173 (pmt170) REVERT: E 12 GLN cc_start: 0.8097 (mp10) cc_final: 0.7821 (mp10) REVERT: R 45 PHE cc_start: 0.7640 (t80) cc_final: 0.7019 (t80) REVERT: R 108 ARG cc_start: 0.7727 (mtp-110) cc_final: 0.6686 (tpt90) REVERT: R 211 TRP cc_start: 0.7099 (t60) cc_final: 0.6782 (t60) outliers start: 12 outliers final: 9 residues processed: 178 average time/residue: 0.2922 time to fit residues: 67.1735 Evaluate side-chains 181 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 230 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 35 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 104 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 225 GLN B 345 ASN G 58 ASN R 214 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.146527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.112857 restraints weight = 33403.942| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.22 r_work: 0.3022 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9379 Z= 0.111 Angle : 0.480 5.434 12709 Z= 0.257 Chirality : 0.040 0.147 1421 Planarity : 0.004 0.044 1616 Dihedral : 4.743 56.253 1266 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.90 % Allowed : 9.87 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.00 (0.25), residues: 1140 helix: 1.95 (0.25), residues: 410 sheet: -0.18 (0.31), residues: 283 loop : 0.17 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 332 TYR 0.016 0.001 TYR E 190 PHE 0.011 0.001 PHE R 338 TRP 0.015 0.001 TRP B 87 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9377) covalent geometry : angle 0.48006 (12705) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.45142 ( 4) hydrogen bonds : bond 0.03909 ( 480) hydrogen bonds : angle 4.90269 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 183 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8371 (mtpp) REVERT: A 226 ASP cc_start: 0.8284 (t70) cc_final: 0.7977 (t70) REVERT: B 239 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: B 254 THR cc_start: 0.8810 (p) cc_final: 0.8581 (p) REVERT: C 0 ARG cc_start: 0.7868 (mtt180) cc_final: 0.5194 (pmt170) REVERT: E 12 GLN cc_start: 0.8108 (mp10) cc_final: 0.7848 (mp10) REVERT: G 51 THR cc_start: 0.7888 (m) cc_final: 0.7684 (p) REVERT: G 61 ARG cc_start: 0.7452 (mmm160) cc_final: 0.6703 (mmt90) REVERT: R 45 PHE cc_start: 0.7714 (t80) cc_final: 0.7082 (t80) REVERT: R 108 ARG cc_start: 0.7667 (mtp-110) cc_final: 0.6753 (tpt90) REVERT: R 211 TRP cc_start: 0.6976 (t60) cc_final: 0.6664 (t60) outliers start: 9 outliers final: 6 residues processed: 188 average time/residue: 0.2961 time to fit residues: 71.4400 Evaluate side-chains 180 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 173 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 214 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 345 ASN G 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.143840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110059 restraints weight = 33313.746| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.24 r_work: 0.2930 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9379 Z= 0.181 Angle : 0.509 5.310 12709 Z= 0.275 Chirality : 0.041 0.144 1421 Planarity : 0.004 0.047 1616 Dihedral : 4.806 56.855 1266 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.10 % Allowed : 10.27 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.95 (0.25), residues: 1140 helix: 1.96 (0.25), residues: 410 sheet: -0.23 (0.31), residues: 275 loop : 0.08 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 332 TYR 0.019 0.001 TYR E 190 PHE 0.011 0.001 PHE B 246 TRP 0.013 0.001 TRP B 87 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9377) covalent geometry : angle 0.50859 (12705) SS BOND : bond 0.00316 ( 2) SS BOND : angle 0.60475 ( 4) hydrogen bonds : bond 0.04133 ( 480) hydrogen bonds : angle 4.95257 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.5723 (mm-30) REVERT: A 25 LYS cc_start: 0.8680 (ttmm) cc_final: 0.8408 (mtpp) REVERT: A 226 ASP cc_start: 0.8393 (t70) cc_final: 0.7815 (t0) REVERT: A 281 GLU cc_start: 0.8268 (mp0) cc_final: 0.7544 (tm-30) REVERT: B 239 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: B 254 THR cc_start: 0.8832 (p) cc_final: 0.8627 (p) REVERT: C 0 ARG cc_start: 0.7905 (mtt180) cc_final: 0.5171 (pmt170) REVERT: E 12 GLN cc_start: 0.8193 (mp10) cc_final: 0.7917 (mp10) REVERT: E 81 GLN cc_start: 0.7890 (tp40) cc_final: 0.7625 (tp40) REVERT: G 51 THR cc_start: 0.8036 (m) cc_final: 0.7794 (p) REVERT: G 61 ARG cc_start: 0.7363 (mmm160) cc_final: 0.6600 (mmt90) REVERT: R 45 PHE cc_start: 0.7736 (t80) cc_final: 0.7082 (t80) REVERT: R 104 TYR cc_start: 0.8472 (t80) cc_final: 0.8269 (t80) REVERT: R 108 ARG cc_start: 0.7830 (mtp-110) cc_final: 0.6792 (tpt90) REVERT: R 211 TRP cc_start: 0.7025 (t60) cc_final: 0.6701 (t60) outliers start: 11 outliers final: 7 residues processed: 179 average time/residue: 0.3109 time to fit residues: 71.3876 Evaluate side-chains 177 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 141 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 345 ASN G 58 ASN R 214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.143865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111432 restraints weight = 33215.536| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.12 r_work: 0.2985 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9379 Z= 0.128 Angle : 0.482 4.729 12709 Z= 0.258 Chirality : 0.040 0.145 1421 Planarity : 0.004 0.052 1616 Dihedral : 4.708 56.781 1266 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.50 % Allowed : 10.87 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.00 (0.25), residues: 1140 helix: 2.10 (0.25), residues: 411 sheet: -0.27 (0.31), residues: 275 loop : 0.05 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 332 TYR 0.016 0.001 TYR E 190 PHE 0.010 0.001 PHE R 338 TRP 0.014 0.001 TRP B 87 HIS 0.003 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9377) covalent geometry : angle 0.48250 (12705) SS BOND : bond 0.00286 ( 2) SS BOND : angle 0.47141 ( 4) hydrogen bonds : bond 0.03847 ( 480) hydrogen bonds : angle 4.87376 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.5730 (mm-30) REVERT: A 25 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8420 (mtpp) REVERT: A 226 ASP cc_start: 0.8339 (t70) cc_final: 0.7791 (t0) REVERT: A 281 GLU cc_start: 0.8246 (mp0) cc_final: 0.7550 (tm-30) REVERT: B 151 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8810 (tt) REVERT: B 239 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: B 254 THR cc_start: 0.8789 (p) cc_final: 0.8580 (p) REVERT: C 0 ARG cc_start: 0.7893 (mtt180) cc_final: 0.5194 (pmt170) REVERT: E 12 GLN cc_start: 0.8150 (mp10) cc_final: 0.7882 (mp10) REVERT: E 81 GLN cc_start: 0.7797 (tp40) cc_final: 0.7596 (tp40) REVERT: G 51 THR cc_start: 0.8054 (m) cc_final: 0.7849 (p) REVERT: G 61 ARG cc_start: 0.7280 (mmm160) cc_final: 0.6598 (mmt90) REVERT: R 45 PHE cc_start: 0.7738 (t80) cc_final: 0.7083 (t80) REVERT: R 108 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.6799 (tpt90) REVERT: R 211 TRP cc_start: 0.6965 (t60) cc_final: 0.6639 (t60) REVERT: R 214 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7521 (t0) REVERT: R 218 GLN cc_start: 0.8367 (mt0) cc_final: 0.8021 (mt0) REVERT: R 227 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8348 (mp) outliers start: 15 outliers final: 8 residues processed: 185 average time/residue: 0.2994 time to fit residues: 70.9890 Evaluate side-chains 186 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 227 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 0.0570 chunk 88 optimal weight: 0.6980 chunk 90 optimal weight: 0.0970 overall best weight: 0.9498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.147383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.114312 restraints weight = 33127.082| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.30 r_work: 0.2954 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9379 Z= 0.115 Angle : 0.477 5.470 12709 Z= 0.255 Chirality : 0.040 0.145 1421 Planarity : 0.004 0.056 1616 Dihedral : 4.636 57.017 1266 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.50 % Allowed : 11.07 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.05 (0.25), residues: 1140 helix: 2.15 (0.25), residues: 411 sheet: -0.21 (0.31), residues: 273 loop : 0.04 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 332 TYR 0.016 0.001 TYR E 190 PHE 0.010 0.001 PHE R 338 TRP 0.013 0.001 TRP B 87 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9377) covalent geometry : angle 0.47663 (12705) SS BOND : bond 0.00272 ( 2) SS BOND : angle 0.46311 ( 4) hydrogen bonds : bond 0.03771 ( 480) hydrogen bonds : angle 4.82491 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.5581 (mm-30) REVERT: A 25 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8413 (mtpp) REVERT: A 226 ASP cc_start: 0.8349 (t70) cc_final: 0.7779 (t0) REVERT: A 281 GLU cc_start: 0.8227 (mp0) cc_final: 0.7484 (tm-30) REVERT: B 151 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8850 (tt) REVERT: B 239 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8461 (m-80) REVERT: B 254 THR cc_start: 0.8817 (p) cc_final: 0.8612 (p) REVERT: B 273 ASN cc_start: 0.8641 (t0) cc_final: 0.8390 (t0) REVERT: E 2 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: E 12 GLN cc_start: 0.8207 (mp10) cc_final: 0.7936 (mp10) REVERT: E 81 GLN cc_start: 0.7806 (tp40) cc_final: 0.7590 (tp40) REVERT: G 51 THR cc_start: 0.7929 (m) cc_final: 0.7727 (p) REVERT: G 61 ARG cc_start: 0.7240 (mmm160) cc_final: 0.6604 (mmt90) REVERT: R 45 PHE cc_start: 0.7724 (t80) cc_final: 0.7067 (t80) REVERT: R 108 ARG cc_start: 0.7807 (mtp-110) cc_final: 0.6760 (tpt90) REVERT: R 211 TRP cc_start: 0.6849 (t60) cc_final: 0.6498 (t60) REVERT: R 218 GLN cc_start: 0.8244 (mt0) cc_final: 0.7827 (mt0) REVERT: R 227 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8342 (mp) outliers start: 15 outliers final: 8 residues processed: 186 average time/residue: 0.2877 time to fit residues: 69.3524 Evaluate side-chains 185 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 227 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 ASN E 179 GLN G 23 ASN G 58 ASN R 73 HIS ** R 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.145075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111684 restraints weight = 33069.216| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.31 r_work: 0.2901 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9379 Z= 0.202 Angle : 0.521 5.415 12709 Z= 0.280 Chirality : 0.041 0.144 1421 Planarity : 0.004 0.060 1616 Dihedral : 4.817 57.203 1266 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.60 % Allowed : 10.77 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.89 (0.25), residues: 1140 helix: 2.05 (0.25), residues: 411 sheet: -0.22 (0.32), residues: 268 loop : -0.15 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 332 TYR 0.020 0.001 TYR E 190 PHE 0.013 0.001 PHE B 246 TRP 0.013 0.001 TRP B 87 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 9377) covalent geometry : angle 0.52133 (12705) SS BOND : bond 0.00305 ( 2) SS BOND : angle 0.75989 ( 4) hydrogen bonds : bond 0.04048 ( 480) hydrogen bonds : angle 4.95068 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.5674 (mm-30) REVERT: A 25 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8457 (mtpp) REVERT: A 226 ASP cc_start: 0.8451 (t70) cc_final: 0.7854 (t0) REVERT: A 281 GLU cc_start: 0.8273 (mp0) cc_final: 0.7516 (tm-30) REVERT: B 151 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8898 (tt) REVERT: B 239 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8489 (m-80) REVERT: B 254 THR cc_start: 0.8804 (p) cc_final: 0.8592 (p) REVERT: E 2 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: E 12 GLN cc_start: 0.8212 (mp10) cc_final: 0.7940 (mp10) REVERT: G 51 THR cc_start: 0.8105 (m) cc_final: 0.7881 (p) REVERT: G 61 ARG cc_start: 0.7225 (mmm160) cc_final: 0.6619 (mmt-90) REVERT: R 45 PHE cc_start: 0.7751 (t80) cc_final: 0.7125 (t80) REVERT: R 108 ARG cc_start: 0.7859 (mtp-110) cc_final: 0.6849 (tpt90) REVERT: R 211 TRP cc_start: 0.6964 (t60) cc_final: 0.6601 (t60) REVERT: R 218 GLN cc_start: 0.8393 (mt0) cc_final: 0.8090 (mt0) REVERT: R 227 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8388 (mp) outliers start: 16 outliers final: 10 residues processed: 181 average time/residue: 0.2609 time to fit residues: 61.7802 Evaluate side-chains 176 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 227 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 ASN E 179 GLN G 23 ASN G 58 ASN R 214 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113717 restraints weight = 33061.515| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.29 r_work: 0.2912 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9379 Z= 0.126 Angle : 0.488 5.450 12709 Z= 0.260 Chirality : 0.040 0.153 1421 Planarity : 0.004 0.066 1616 Dihedral : 4.675 57.024 1266 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.60 % Allowed : 11.76 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.99 (0.25), residues: 1140 helix: 2.19 (0.25), residues: 411 sheet: -0.16 (0.32), residues: 266 loop : -0.16 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 332 TYR 0.016 0.001 TYR E 190 PHE 0.010 0.001 PHE R 338 TRP 0.015 0.001 TRP B 87 HIS 0.003 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9377) covalent geometry : angle 0.48812 (12705) SS BOND : bond 0.00301 ( 2) SS BOND : angle 0.48910 ( 4) hydrogen bonds : bond 0.03736 ( 480) hydrogen bonds : angle 4.84671 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.5594 (mm-30) REVERT: A 25 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8446 (mtpp) REVERT: A 226 ASP cc_start: 0.8385 (t70) cc_final: 0.7806 (t0) REVERT: A 281 GLU cc_start: 0.8258 (mp0) cc_final: 0.7523 (tm-30) REVERT: B 151 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8883 (tt) REVERT: B 239 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: B 254 THR cc_start: 0.8799 (p) cc_final: 0.8594 (p) REVERT: E 2 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: E 12 GLN cc_start: 0.8191 (mp10) cc_final: 0.7924 (mp10) REVERT: G 51 THR cc_start: 0.8042 (m) cc_final: 0.7840 (p) REVERT: G 61 ARG cc_start: 0.7055 (mmm160) cc_final: 0.6399 (mmt-90) REVERT: R 45 PHE cc_start: 0.7712 (t80) cc_final: 0.7095 (t80) REVERT: R 108 ARG cc_start: 0.7759 (mtp-110) cc_final: 0.6831 (tpt90) REVERT: R 211 TRP cc_start: 0.6843 (t60) cc_final: 0.6473 (t60) REVERT: R 214 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7670 (t0) REVERT: R 218 GLN cc_start: 0.8432 (mt0) cc_final: 0.8159 (mt0) REVERT: R 227 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8383 (mp) outliers start: 16 outliers final: 9 residues processed: 178 average time/residue: 0.2620 time to fit residues: 60.3262 Evaluate side-chains 177 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 214 ASN Chi-restraints excluded: chain R residue 227 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN B 345 ASN C 9 ASN G 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.146616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113511 restraints weight = 33134.498| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.29 r_work: 0.2978 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9379 Z= 0.149 Angle : 0.501 5.276 12709 Z= 0.268 Chirality : 0.040 0.162 1421 Planarity : 0.004 0.066 1616 Dihedral : 4.678 57.336 1266 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.50 % Allowed : 12.36 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.95 (0.25), residues: 1140 helix: 2.16 (0.25), residues: 411 sheet: -0.19 (0.32), residues: 266 loop : -0.19 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 332 TYR 0.017 0.001 TYR E 190 PHE 0.021 0.001 PHE R 293 TRP 0.013 0.001 TRP B 87 HIS 0.003 0.001 HIS B 316 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9377) covalent geometry : angle 0.50081 (12705) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.58427 ( 4) hydrogen bonds : bond 0.03835 ( 480) hydrogen bonds : angle 4.87539 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.5691 (mm-30) REVERT: A 25 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8450 (mtpp) REVERT: A 226 ASP cc_start: 0.8394 (t70) cc_final: 0.7846 (t0) REVERT: A 281 GLU cc_start: 0.8230 (mp0) cc_final: 0.7565 (tm-30) REVERT: B 151 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8881 (tt) REVERT: B 239 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: B 254 THR cc_start: 0.8785 (p) cc_final: 0.8571 (p) REVERT: E 2 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: E 12 GLN cc_start: 0.8164 (mp10) cc_final: 0.7898 (mp10) REVERT: G 61 ARG cc_start: 0.7009 (mmm160) cc_final: 0.6403 (mmt-90) REVERT: R 45 PHE cc_start: 0.7800 (t80) cc_final: 0.7196 (t80) REVERT: R 104 TYR cc_start: 0.8316 (t80) cc_final: 0.7864 (t80) REVERT: R 108 ARG cc_start: 0.7768 (mtp-110) cc_final: 0.6834 (tpt90) REVERT: R 211 TRP cc_start: 0.6929 (t60) cc_final: 0.6569 (t60) REVERT: R 218 GLN cc_start: 0.8252 (mt0) cc_final: 0.7831 (mt0) REVERT: R 227 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8395 (mp) outliers start: 15 outliers final: 9 residues processed: 175 average time/residue: 0.2759 time to fit residues: 62.8869 Evaluate side-chains 176 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain E residue 2 GLN Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 110 TYR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 227 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 71 optimal weight: 0.0470 chunk 94 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN B 345 ASN G 58 ASN R 214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.148262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.115469 restraints weight = 33158.680| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.20 r_work: 0.2969 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9379 Z= 0.100 Angle : 0.473 5.230 12709 Z= 0.252 Chirality : 0.040 0.146 1421 Planarity : 0.004 0.064 1616 Dihedral : 4.521 57.747 1266 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.40 % Allowed : 12.66 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.09 (0.25), residues: 1140 helix: 2.33 (0.25), residues: 411 sheet: -0.17 (0.32), residues: 266 loop : -0.11 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 332 TYR 0.013 0.001 TYR E 190 PHE 0.009 0.001 PHE R 338 TRP 0.014 0.001 TRP B 87 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9377) covalent geometry : angle 0.47314 (12705) SS BOND : bond 0.00277 ( 2) SS BOND : angle 0.39310 ( 4) hydrogen bonds : bond 0.03517 ( 480) hydrogen bonds : angle 4.75071 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5568.29 seconds wall clock time: 95 minutes 2.02 seconds (5702.02 seconds total)