Starting phenix.real_space_refine on Thu Mar 13 14:55:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kfx_37207/03_2025/8kfx_37207.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kfx_37207/03_2025/8kfx_37207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kfx_37207/03_2025/8kfx_37207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kfx_37207/03_2025/8kfx_37207.map" model { file = "/net/cci-nas-00/data/ceres_data/8kfx_37207/03_2025/8kfx_37207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kfx_37207/03_2025/8kfx_37207.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5762 2.51 5 N 1506 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9001 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1812 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2342 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 5, 'TRANS': 282} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'OS9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.53, per 1000 atoms: 0.61 Number of scatterers: 9001 At special positions: 0 Unit cell: (89.44, 121.68, 130, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1667 8.00 N 1506 7.00 C 5762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 2.35 Conformation dependent library (CDL) restraints added in 1.0 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 39.4% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.534A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.666A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.962A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.727A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.663A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'R' and resid 31 through 62 Processing helix chain 'R' and resid 68 through 86 Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.749A pdb=" N LYS R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 170 Proline residue: R 167 - end of helix removed outlier: 3.777A pdb=" N VAL R 170 " --> pdb=" O ILE R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 205 removed outlier: 3.537A pdb=" N LYS R 195 " --> pdb=" O THR R 191 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET R 202 " --> pdb=" O THR R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 227 removed outlier: 3.523A pdb=" N ARG R 227 " --> pdb=" O HIS R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 266 Proline residue: R 253 - end of helix Processing helix chain 'R' and resid 271 through 291 Processing helix chain 'R' and resid 291 through 301 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.785A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.520A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.800A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.512A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.552A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.339A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.620A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.927A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.704A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.538A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.301A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.632A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 172 through 177 Processing sheet with id=AB1, first strand: chain 'S' and resid 6 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.814A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.843A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1320 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: 2.67 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2861 1.34 - 1.46: 2235 1.46 - 1.58: 4001 1.58 - 1.70: 1 1.70 - 1.82: 95 Bond restraints: 9193 Sorted by residual: bond pdb=" N PRO S 224 " pdb=" CD PRO S 224 " ideal model delta sigma weight residual 1.473 1.624 -0.151 1.40e-02 5.10e+03 1.17e+02 bond pdb=" N ARG S 67 " pdb=" CA ARG S 67 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.06e+00 bond pdb=" N PHE R 290 " pdb=" CA PHE R 290 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.31e-02 5.83e+03 7.05e+00 bond pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.29e-02 6.01e+03 6.69e+00 bond pdb=" N SER R 289 " pdb=" CA SER R 289 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.18e-02 7.18e+03 5.73e+00 ... (remaining 9188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 12301 2.29 - 4.57: 119 4.57 - 6.86: 18 6.86 - 9.15: 5 9.15 - 11.43: 1 Bond angle restraints: 12444 Sorted by residual: angle pdb=" N THR R 291 " pdb=" CA THR R 291 " pdb=" C THR R 291 " ideal model delta sigma weight residual 112.34 107.46 4.88 1.30e+00 5.92e-01 1.41e+01 angle pdb=" CA GLN A 52 " pdb=" CB GLN A 52 " pdb=" CG GLN A 52 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta sigma weight residual 121.80 113.02 8.78 2.44e+00 1.68e-01 1.29e+01 angle pdb=" CA PHE R 290 " pdb=" CB PHE R 290 " pdb=" CG PHE R 290 " ideal model delta sigma weight residual 113.80 117.11 -3.31 1.00e+00 1.00e+00 1.10e+01 angle pdb=" CA LEU R 205 " pdb=" CB LEU R 205 " pdb=" CG LEU R 205 " ideal model delta sigma weight residual 116.30 127.73 -11.43 3.50e+00 8.16e-02 1.07e+01 ... (remaining 12439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4718 17.91 - 35.82: 558 35.82 - 53.73: 162 53.73 - 71.65: 22 71.65 - 89.56: 5 Dihedral angle restraints: 5465 sinusoidal: 2151 harmonic: 3314 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 180.00 134.90 45.10 0 5.00e+00 4.00e-02 8.14e+01 dihedral pdb=" CA ARG S 179 " pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 821 0.028 - 0.057: 354 0.057 - 0.085: 154 0.085 - 0.114: 71 0.114 - 0.142: 14 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB ILE S 70 " pdb=" CA ILE S 70 " pdb=" CG1 ILE S 70 " pdb=" CG2 ILE S 70 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA PHE R 41 " pdb=" N PHE R 41 " pdb=" C PHE R 41 " pdb=" CB PHE R 41 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 1411 not shown) Planarity restraints: 1558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.040 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO S 224 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 186 " -0.011 2.00e-02 2.50e+03 1.64e-02 4.71e+00 pdb=" CG PHE R 186 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE R 186 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE R 186 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE R 186 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 186 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 186 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 170 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" CG ASP B 170 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP B 170 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 170 " -0.012 2.00e-02 2.50e+03 ... (remaining 1555 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 554 2.73 - 3.27: 8901 3.27 - 3.82: 15392 3.82 - 4.36: 18481 4.36 - 4.90: 31911 Nonbonded interactions: 75239 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.189 3.040 nonbonded pdb=" O LEU R 50 " pdb=" OG SER R 54 " model vdw 2.204 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.208 3.040 nonbonded pdb=" ND1 HIS B 54 " pdb=" OG SER B 74 " model vdw 2.252 3.120 nonbonded pdb=" N GLU A 297 " pdb=" OE1 GLU A 297 " model vdw 2.267 3.120 ... (remaining 75234 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: 2.430 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.004 0.151 9193 Z= 0.253 Angle : 0.613 11.433 12444 Z= 0.329 Chirality : 0.042 0.142 1414 Planarity : 0.004 0.058 1558 Dihedral : 16.545 89.558 3318 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.51 % Allowed : 30.16 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1125 helix: 2.18 (0.27), residues: 398 sheet: 0.30 (0.30), residues: 286 loop : -0.64 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 251 HIS 0.005 0.001 HIS S 35 PHE 0.037 0.002 PHE R 186 TYR 0.016 0.001 TYR R 94 ARG 0.013 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 252 time to evaluate : 0.984 Fit side-chains REVERT: A 231 ASP cc_start: 0.7629 (t0) cc_final: 0.7403 (t0) REVERT: A 340 THR cc_start: 0.8656 (m) cc_final: 0.8351 (t) REVERT: B 19 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7279 (mtm110) REVERT: B 61 MET cc_start: 0.8231 (tmm) cc_final: 0.7993 (ppp) REVERT: R 117 PHE cc_start: 0.8151 (t80) cc_final: 0.7919 (t80) REVERT: R 121 MET cc_start: 0.8187 (tpp) cc_final: 0.7617 (mpp) REVERT: R 216 PHE cc_start: 0.8045 (t80) cc_final: 0.7738 (t80) outliers start: 5 outliers final: 4 residues processed: 256 average time/residue: 1.1428 time to fit residues: 313.2795 Evaluate side-chains 246 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 242 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain S residue 130 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 75 GLN B 220 GLN R 203 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.125802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107297 restraints weight = 12953.483| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.96 r_work: 0.3263 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9193 Z= 0.352 Angle : 0.591 10.234 12444 Z= 0.315 Chirality : 0.044 0.170 1414 Planarity : 0.004 0.062 1558 Dihedral : 5.530 47.291 1276 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.55 % Allowed : 24.80 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1125 helix: 2.12 (0.26), residues: 399 sheet: 0.26 (0.30), residues: 288 loop : -0.66 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.026 0.002 PHE R 290 TYR 0.015 0.002 TYR A 320 ARG 0.005 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.983 Fit side-chains REVERT: A 49 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.5990 (mp) REVERT: A 186 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6372 (tm-30) REVERT: A 193 ASP cc_start: 0.8032 (m-30) cc_final: 0.7800 (t0) REVERT: A 197 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8224 (mtpp) REVERT: A 231 ASP cc_start: 0.7938 (t0) cc_final: 0.7684 (t0) REVERT: A 269 ASN cc_start: 0.8408 (m-40) cc_final: 0.8172 (m110) REVERT: B 19 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7216 (ttp80) REVERT: B 22 ARG cc_start: 0.7283 (mtt180) cc_final: 0.7032 (mtp180) REVERT: B 61 MET cc_start: 0.8209 (tmm) cc_final: 0.7991 (ppp) REVERT: B 197 ARG cc_start: 0.7856 (mpt-90) cc_final: 0.7625 (mtt-85) REVERT: B 219 ARG cc_start: 0.8247 (mtp85) cc_final: 0.8006 (mtt-85) REVERT: B 234 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8489 (OUTLIER) REVERT: B 258 ASP cc_start: 0.8042 (t0) cc_final: 0.7274 (t0) REVERT: R 37 LEU cc_start: 0.8501 (tp) cc_final: 0.7976 (tm) REVERT: R 41 PHE cc_start: 0.7826 (m-80) cc_final: 0.7310 (m-80) REVERT: R 46 PHE cc_start: 0.7731 (t80) cc_final: 0.7384 (t80) REVERT: R 55 LEU cc_start: 0.8267 (tm) cc_final: 0.7966 (tt) REVERT: R 95 LEU cc_start: 0.8662 (mt) cc_final: 0.8438 (mm) REVERT: R 105 MET cc_start: 0.7831 (mmm) cc_final: 0.7439 (tmm) REVERT: S 39 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8008 (tp40) REVERT: S 69 THR cc_start: 0.8188 (p) cc_final: 0.7952 (t) REVERT: S 110 PHE cc_start: 0.8658 (t80) cc_final: 0.8330 (t80) REVERT: S 200 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: S 223 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7557 (t80) outliers start: 45 outliers final: 22 residues processed: 278 average time/residue: 1.1080 time to fit residues: 329.8954 Evaluate side-chains 270 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 200 PHE Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 75 GLN B 220 GLN R 203 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.126378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107731 restraints weight = 13102.122| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.98 r_work: 0.3268 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9193 Z= 0.285 Angle : 0.550 10.840 12444 Z= 0.292 Chirality : 0.042 0.152 1414 Planarity : 0.004 0.063 1558 Dihedral : 5.480 53.399 1271 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.66 % Allowed : 24.29 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1125 helix: 2.21 (0.26), residues: 400 sheet: 0.14 (0.29), residues: 299 loop : -0.68 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.027 0.002 PHE R 117 TYR 0.016 0.002 TYR S 178 ARG 0.006 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 1.130 Fit side-chains REVERT: A 49 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.5738 (mp) REVERT: A 186 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6817 (mm-30) REVERT: A 193 ASP cc_start: 0.8007 (m-30) cc_final: 0.7785 (t0) REVERT: A 197 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8302 (mtpp) REVERT: A 231 ASP cc_start: 0.7981 (t0) cc_final: 0.7692 (t0) REVERT: A 269 ASN cc_start: 0.8461 (m-40) cc_final: 0.8219 (m110) REVERT: A 310 LEU cc_start: 0.8714 (mt) cc_final: 0.8505 (mp) REVERT: B 19 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7217 (ttp80) REVERT: B 22 ARG cc_start: 0.7286 (mtt180) cc_final: 0.7003 (mtp180) REVERT: B 61 MET cc_start: 0.8216 (tmm) cc_final: 0.7994 (ppp) REVERT: B 76 ASP cc_start: 0.7659 (p0) cc_final: 0.7389 (p0) REVERT: B 197 ARG cc_start: 0.7899 (mpt-90) cc_final: 0.7594 (mtt-85) REVERT: B 214 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7526 (mmt180) REVERT: B 219 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7996 (mtt-85) REVERT: B 258 ASP cc_start: 0.8104 (t0) cc_final: 0.7222 (t0) REVERT: R 37 LEU cc_start: 0.8460 (tp) cc_final: 0.7974 (tm) REVERT: R 41 PHE cc_start: 0.7924 (m-80) cc_final: 0.7475 (m-80) REVERT: R 46 PHE cc_start: 0.7684 (t80) cc_final: 0.7293 (t80) REVERT: R 55 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7949 (tt) REVERT: R 95 LEU cc_start: 0.8658 (mt) cc_final: 0.8451 (mm) REVERT: R 105 MET cc_start: 0.7872 (mmm) cc_final: 0.7401 (tmm) REVERT: R 220 LYS cc_start: 0.8322 (mmmm) cc_final: 0.7996 (mmmm) REVERT: S 39 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8026 (tp40) REVERT: S 69 THR cc_start: 0.8203 (p) cc_final: 0.7964 (t) REVERT: S 110 PHE cc_start: 0.8636 (t80) cc_final: 0.8328 (t80) REVERT: S 205 SER cc_start: 0.8002 (m) cc_final: 0.7662 (p) REVERT: S 223 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7571 (t80) outliers start: 46 outliers final: 22 residues processed: 274 average time/residue: 1.1745 time to fit residues: 343.9485 Evaluate side-chains 269 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 0.0470 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 75 GLN B 220 GLN B 259 GLN ** R 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108719 restraints weight = 13090.177| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.97 r_work: 0.3289 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9193 Z= 0.205 Angle : 0.520 8.734 12444 Z= 0.275 Chirality : 0.040 0.141 1414 Planarity : 0.004 0.062 1558 Dihedral : 5.346 54.441 1271 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.77 % Allowed : 23.68 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1125 helix: 2.31 (0.26), residues: 407 sheet: 0.20 (0.29), residues: 297 loop : -0.63 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.024 0.002 PHE R 117 TYR 0.016 0.001 TYR S 178 ARG 0.008 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 49 ILE cc_start: 0.6702 (OUTLIER) cc_final: 0.5797 (mp) REVERT: A 193 ASP cc_start: 0.7999 (m-30) cc_final: 0.7785 (t0) REVERT: A 231 ASP cc_start: 0.7951 (t0) cc_final: 0.7670 (t0) REVERT: A 269 ASN cc_start: 0.8464 (m-40) cc_final: 0.8213 (m110) REVERT: B 19 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7183 (ttp80) REVERT: B 22 ARG cc_start: 0.7261 (mtt180) cc_final: 0.7011 (mtp180) REVERT: B 61 MET cc_start: 0.8212 (tmm) cc_final: 0.7990 (ppp) REVERT: B 76 ASP cc_start: 0.7633 (p0) cc_final: 0.7348 (p0) REVERT: B 130 GLU cc_start: 0.8169 (mp0) cc_final: 0.7707 (mp0) REVERT: B 197 ARG cc_start: 0.7919 (mpt-90) cc_final: 0.7580 (mtt-85) REVERT: B 214 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7512 (mmt180) REVERT: B 219 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7960 (mtt-85) REVERT: B 258 ASP cc_start: 0.8097 (t0) cc_final: 0.7154 (t0) REVERT: R 37 LEU cc_start: 0.8422 (tp) cc_final: 0.8017 (tm) REVERT: R 41 PHE cc_start: 0.7942 (m-80) cc_final: 0.7508 (m-80) REVERT: R 46 PHE cc_start: 0.7735 (t80) cc_final: 0.7403 (t80) REVERT: R 55 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7943 (tt) REVERT: R 95 LEU cc_start: 0.8649 (mt) cc_final: 0.8423 (mm) REVERT: R 105 MET cc_start: 0.7856 (mmm) cc_final: 0.7412 (mmm) REVERT: R 219 ILE cc_start: 0.8566 (mm) cc_final: 0.8353 (mt) REVERT: R 220 LYS cc_start: 0.8286 (mmmm) cc_final: 0.8033 (mmmm) REVERT: S 39 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7999 (tp40) REVERT: S 69 THR cc_start: 0.8229 (p) cc_final: 0.7988 (t) REVERT: S 110 PHE cc_start: 0.8614 (t80) cc_final: 0.8336 (t80) REVERT: S 205 SER cc_start: 0.8005 (m) cc_final: 0.7655 (p) REVERT: S 223 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.7548 (t80) outliers start: 57 outliers final: 25 residues processed: 281 average time/residue: 1.1136 time to fit residues: 334.7896 Evaluate side-chains 281 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 65 optimal weight: 0.0370 chunk 59 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 74 optimal weight: 0.0980 chunk 100 optimal weight: 0.0050 overall best weight: 0.2872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109752 restraints weight = 12946.682| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.98 r_work: 0.3299 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9193 Z= 0.153 Angle : 0.501 7.759 12444 Z= 0.263 Chirality : 0.039 0.139 1414 Planarity : 0.004 0.061 1558 Dihedral : 5.224 58.214 1271 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.36 % Allowed : 24.70 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1125 helix: 2.46 (0.26), residues: 408 sheet: 0.23 (0.29), residues: 297 loop : -0.60 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.021 0.001 PHE R 117 TYR 0.017 0.001 TYR S 178 ARG 0.009 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 262 time to evaluate : 1.013 Fit side-chains REVERT: A 49 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.5619 (mp) REVERT: A 193 ASP cc_start: 0.8027 (m-30) cc_final: 0.7802 (t0) REVERT: A 197 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8249 (mtpp) REVERT: A 231 ASP cc_start: 0.7927 (t0) cc_final: 0.7629 (t0) REVERT: A 269 ASN cc_start: 0.8457 (m-40) cc_final: 0.8212 (m110) REVERT: A 318 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: B 19 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7190 (ttp80) REVERT: B 22 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6980 (mtp180) REVERT: B 61 MET cc_start: 0.8206 (tmm) cc_final: 0.7976 (ppp) REVERT: B 76 ASP cc_start: 0.7607 (p0) cc_final: 0.7333 (p0) REVERT: B 130 GLU cc_start: 0.8165 (mp0) cc_final: 0.7723 (mp0) REVERT: B 197 ARG cc_start: 0.7905 (mpt-90) cc_final: 0.7582 (mtt-85) REVERT: B 214 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7538 (mmt180) REVERT: B 258 ASP cc_start: 0.8054 (t0) cc_final: 0.7169 (t0) REVERT: B 283 ARG cc_start: 0.8600 (tpt90) cc_final: 0.8209 (tpt170) REVERT: R 37 LEU cc_start: 0.8402 (tp) cc_final: 0.7961 (tm) REVERT: R 41 PHE cc_start: 0.7941 (m-80) cc_final: 0.7528 (m-80) REVERT: R 46 PHE cc_start: 0.7708 (t80) cc_final: 0.7313 (t80) REVERT: R 49 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8304 (p) REVERT: R 55 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7883 (tt) REVERT: R 95 LEU cc_start: 0.8666 (mt) cc_final: 0.8457 (mm) REVERT: R 105 MET cc_start: 0.7826 (mmm) cc_final: 0.7424 (mmm) REVERT: R 121 MET cc_start: 0.8213 (tpp) cc_final: 0.7464 (mpp) REVERT: R 219 ILE cc_start: 0.8576 (mm) cc_final: 0.8346 (mt) REVERT: R 220 LYS cc_start: 0.8332 (mmmm) cc_final: 0.7990 (mmmm) REVERT: S 39 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8024 (tp40) REVERT: S 69 THR cc_start: 0.8226 (p) cc_final: 0.7977 (t) REVERT: S 110 PHE cc_start: 0.8594 (t80) cc_final: 0.8387 (t80) REVERT: S 205 SER cc_start: 0.8000 (m) cc_final: 0.7601 (p) REVERT: S 223 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7545 (t80) outliers start: 53 outliers final: 23 residues processed: 285 average time/residue: 1.1607 time to fit residues: 356.0107 Evaluate side-chains 280 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN R 203 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108833 restraints weight = 12978.005| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.99 r_work: 0.3283 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9193 Z= 0.240 Angle : 0.526 7.606 12444 Z= 0.277 Chirality : 0.041 0.139 1414 Planarity : 0.004 0.063 1558 Dihedral : 5.015 47.420 1269 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.55 % Allowed : 26.92 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1125 helix: 2.39 (0.26), residues: 408 sheet: 0.21 (0.29), residues: 297 loop : -0.57 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.025 0.002 PHE R 186 TYR 0.014 0.001 TYR S 178 ARG 0.011 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 1.152 Fit side-chains REVERT: A 49 ILE cc_start: 0.6557 (OUTLIER) cc_final: 0.5699 (mp) REVERT: A 193 ASP cc_start: 0.8020 (m-30) cc_final: 0.7799 (t0) REVERT: A 197 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8280 (mtpp) REVERT: A 231 ASP cc_start: 0.7932 (t0) cc_final: 0.7607 (t0) REVERT: A 269 ASN cc_start: 0.8493 (m-40) cc_final: 0.8236 (m110) REVERT: A 318 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: B 22 ARG cc_start: 0.7243 (mtt180) cc_final: 0.7041 (mtp180) REVERT: B 61 MET cc_start: 0.8216 (tmm) cc_final: 0.7992 (ppp) REVERT: B 76 ASP cc_start: 0.7595 (p0) cc_final: 0.7343 (p0) REVERT: B 130 GLU cc_start: 0.8171 (mp0) cc_final: 0.7725 (mp0) REVERT: B 197 ARG cc_start: 0.7892 (mpt-90) cc_final: 0.7568 (mtt-85) REVERT: B 214 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7513 (mmt180) REVERT: B 258 ASP cc_start: 0.8062 (t0) cc_final: 0.7252 (t0) REVERT: R 37 LEU cc_start: 0.8404 (tp) cc_final: 0.7955 (tm) REVERT: R 41 PHE cc_start: 0.7946 (m-80) cc_final: 0.7548 (m-80) REVERT: R 46 PHE cc_start: 0.7726 (t80) cc_final: 0.7338 (t80) REVERT: R 49 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8339 (p) REVERT: R 55 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7922 (tt) REVERT: R 95 LEU cc_start: 0.8664 (mt) cc_final: 0.8431 (mm) REVERT: R 105 MET cc_start: 0.7904 (mmm) cc_final: 0.7464 (mmm) REVERT: R 235 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7367 (mmmm) REVERT: R 298 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8248 (t) REVERT: S 39 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7997 (tp40) REVERT: S 69 THR cc_start: 0.8186 (p) cc_final: 0.7948 (t) REVERT: S 110 PHE cc_start: 0.8614 (t80) cc_final: 0.8377 (t80) REVERT: S 205 SER cc_start: 0.8002 (m) cc_final: 0.7581 (p) REVERT: S 223 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7538 (t80) outliers start: 45 outliers final: 22 residues processed: 277 average time/residue: 1.1588 time to fit residues: 344.4701 Evaluate side-chains 284 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN R 203 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108527 restraints weight = 13084.217| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.97 r_work: 0.3279 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9193 Z= 0.288 Angle : 0.546 7.805 12444 Z= 0.288 Chirality : 0.042 0.143 1414 Planarity : 0.004 0.064 1558 Dihedral : 5.226 53.286 1269 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.06 % Allowed : 26.42 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1125 helix: 2.34 (0.26), residues: 402 sheet: 0.17 (0.29), residues: 297 loop : -0.56 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.021 0.002 PHE R 216 TYR 0.013 0.002 TYR R 93 ARG 0.010 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 0.953 Fit side-chains REVERT: A 49 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.5725 (mp) REVERT: A 186 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6688 (mm-30) REVERT: A 193 ASP cc_start: 0.7971 (m-30) cc_final: 0.7752 (t0) REVERT: A 197 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8267 (mtpp) REVERT: A 231 ASP cc_start: 0.7921 (t0) cc_final: 0.7621 (t0) REVERT: A 269 ASN cc_start: 0.8482 (m-40) cc_final: 0.8232 (m110) REVERT: A 318 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: B 19 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7479 (mtm110) REVERT: B 22 ARG cc_start: 0.7320 (mtt180) cc_final: 0.7053 (mtp180) REVERT: B 61 MET cc_start: 0.8188 (tmm) cc_final: 0.7973 (ppp) REVERT: B 76 ASP cc_start: 0.7596 (p0) cc_final: 0.7330 (p0) REVERT: B 130 GLU cc_start: 0.8186 (mp0) cc_final: 0.7726 (mp0) REVERT: B 197 ARG cc_start: 0.7886 (mpt-90) cc_final: 0.7556 (mtt-85) REVERT: B 214 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7556 (mmt180) REVERT: B 258 ASP cc_start: 0.8067 (t0) cc_final: 0.7350 (t0) REVERT: R 37 LEU cc_start: 0.8399 (tp) cc_final: 0.7971 (tm) REVERT: R 41 PHE cc_start: 0.7962 (m-80) cc_final: 0.7571 (m-80) REVERT: R 46 PHE cc_start: 0.7808 (t80) cc_final: 0.7404 (t80) REVERT: R 49 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8365 (p) REVERT: R 55 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7951 (tt) REVERT: R 95 LEU cc_start: 0.8628 (mt) cc_final: 0.8313 (mm) REVERT: R 105 MET cc_start: 0.7915 (mmm) cc_final: 0.7483 (mmm) REVERT: R 121 MET cc_start: 0.8152 (tpp) cc_final: 0.7584 (mpp) REVERT: R 168 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7654 (mp) REVERT: R 235 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7347 (mmmm) REVERT: R 298 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8281 (t) REVERT: S 39 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8025 (tp40) REVERT: S 69 THR cc_start: 0.8160 (p) cc_final: 0.7942 (t) REVERT: S 205 SER cc_start: 0.7995 (m) cc_final: 0.7629 (p) REVERT: S 223 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7511 (t80) outliers start: 50 outliers final: 22 residues processed: 282 average time/residue: 1.1456 time to fit residues: 346.1067 Evaluate side-chains 280 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 101 optimal weight: 0.0870 chunk 89 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.127117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108856 restraints weight = 13142.904| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.97 r_work: 0.3283 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9193 Z= 0.228 Angle : 0.538 7.708 12444 Z= 0.283 Chirality : 0.041 0.150 1414 Planarity : 0.004 0.062 1558 Dihedral : 5.234 55.615 1269 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.66 % Allowed : 26.62 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1125 helix: 2.29 (0.26), residues: 408 sheet: 0.16 (0.29), residues: 297 loop : -0.52 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 251 HIS 0.005 0.001 HIS S 35 PHE 0.023 0.002 PHE R 186 TYR 0.014 0.001 TYR S 178 ARG 0.008 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.941 Fit side-chains REVERT: A 49 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.5729 (mp) REVERT: A 186 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6648 (mm-30) REVERT: A 193 ASP cc_start: 0.7958 (m-30) cc_final: 0.7737 (t0) REVERT: A 197 LYS cc_start: 0.8499 (mtmm) cc_final: 0.8276 (mtpp) REVERT: A 231 ASP cc_start: 0.7896 (t0) cc_final: 0.7602 (t0) REVERT: A 269 ASN cc_start: 0.8440 (m-40) cc_final: 0.8193 (m110) REVERT: A 318 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: A 328 ASP cc_start: 0.7815 (m-30) cc_final: 0.7480 (m-30) REVERT: B 22 ARG cc_start: 0.7299 (mtt180) cc_final: 0.7033 (mtp180) REVERT: B 30 LEU cc_start: 0.7887 (tp) cc_final: 0.7585 (tt) REVERT: B 61 MET cc_start: 0.8188 (tmm) cc_final: 0.7965 (ppp) REVERT: B 76 ASP cc_start: 0.7580 (p0) cc_final: 0.7344 (p0) REVERT: B 130 GLU cc_start: 0.8182 (mp0) cc_final: 0.7743 (mp0) REVERT: B 197 ARG cc_start: 0.7862 (mpt-90) cc_final: 0.7540 (mtt-85) REVERT: B 214 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7547 (mmt180) REVERT: B 258 ASP cc_start: 0.8039 (t0) cc_final: 0.7293 (t0) REVERT: R 37 LEU cc_start: 0.8358 (tp) cc_final: 0.7927 (tm) REVERT: R 41 PHE cc_start: 0.7969 (m-80) cc_final: 0.7576 (m-80) REVERT: R 46 PHE cc_start: 0.7720 (t80) cc_final: 0.7346 (t80) REVERT: R 49 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8360 (p) REVERT: R 55 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7950 (tt) REVERT: R 95 LEU cc_start: 0.8633 (mt) cc_final: 0.8402 (mm) REVERT: R 105 MET cc_start: 0.7893 (mmm) cc_final: 0.7499 (mmm) REVERT: R 121 MET cc_start: 0.8163 (tpp) cc_final: 0.7466 (mpp) REVERT: R 168 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7673 (mp) REVERT: R 235 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7375 (mmmm) REVERT: R 298 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8260 (t) REVERT: S 39 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7928 (tp40) REVERT: S 69 THR cc_start: 0.8177 (p) cc_final: 0.7959 (t) REVERT: S 205 SER cc_start: 0.7996 (m) cc_final: 0.7622 (p) REVERT: S 223 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7492 (t80) outliers start: 46 outliers final: 26 residues processed: 278 average time/residue: 1.0623 time to fit residues: 317.2097 Evaluate side-chains 284 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.0000 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 26 optimal weight: 0.0770 chunk 86 optimal weight: 0.7980 overall best weight: 0.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109490 restraints weight = 12998.933| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.98 r_work: 0.3297 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9193 Z= 0.168 Angle : 0.520 7.545 12444 Z= 0.274 Chirality : 0.040 0.142 1414 Planarity : 0.004 0.060 1558 Dihedral : 5.129 56.181 1269 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.45 % Allowed : 27.02 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1125 helix: 2.35 (0.26), residues: 408 sheet: 0.15 (0.29), residues: 299 loop : -0.46 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 251 HIS 0.005 0.001 HIS S 35 PHE 0.022 0.001 PHE R 216 TYR 0.016 0.001 TYR S 178 ARG 0.008 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 1.022 Fit side-chains REVERT: A 186 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6632 (mm-30) REVERT: A 193 ASP cc_start: 0.8011 (m-30) cc_final: 0.7790 (t0) REVERT: A 197 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8272 (mtpp) REVERT: A 231 ASP cc_start: 0.7805 (t0) cc_final: 0.7493 (t0) REVERT: A 269 ASN cc_start: 0.8448 (m-40) cc_final: 0.8164 (m110) REVERT: A 318 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: A 328 ASP cc_start: 0.7819 (m-30) cc_final: 0.7589 (m-30) REVERT: A 340 THR cc_start: 0.8641 (m) cc_final: 0.8296 (t) REVERT: B 19 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7479 (mtm110) REVERT: B 22 ARG cc_start: 0.7249 (mtt180) cc_final: 0.7036 (mtp180) REVERT: B 30 LEU cc_start: 0.7791 (tp) cc_final: 0.7480 (tt) REVERT: B 61 MET cc_start: 0.8238 (tmm) cc_final: 0.7995 (ppp) REVERT: B 76 ASP cc_start: 0.7577 (p0) cc_final: 0.7326 (p0) REVERT: B 130 GLU cc_start: 0.8162 (mp0) cc_final: 0.7743 (mp0) REVERT: B 197 ARG cc_start: 0.7889 (mpt-90) cc_final: 0.7558 (mtt-85) REVERT: B 214 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7522 (mmt180) REVERT: B 258 ASP cc_start: 0.8023 (t0) cc_final: 0.7349 (t0) REVERT: R 37 LEU cc_start: 0.8338 (tp) cc_final: 0.7903 (tm) REVERT: R 41 PHE cc_start: 0.7959 (m-80) cc_final: 0.7551 (m-80) REVERT: R 46 PHE cc_start: 0.7749 (t80) cc_final: 0.7366 (t80) REVERT: R 49 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8357 (p) REVERT: R 55 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7917 (tt) REVERT: R 95 LEU cc_start: 0.8617 (mt) cc_final: 0.8382 (mm) REVERT: R 105 MET cc_start: 0.7874 (mmm) cc_final: 0.7494 (mmm) REVERT: R 121 MET cc_start: 0.8166 (tpp) cc_final: 0.7487 (mpp) REVERT: R 168 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7687 (mp) REVERT: R 235 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7336 (mmmm) REVERT: R 298 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8241 (t) REVERT: S 39 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8081 (tp40) REVERT: S 69 THR cc_start: 0.8212 (p) cc_final: 0.7975 (t) REVERT: S 98 ARG cc_start: 0.8672 (ptm160) cc_final: 0.8377 (ptm160) REVERT: S 205 SER cc_start: 0.8012 (m) cc_final: 0.7590 (p) REVERT: S 223 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7474 (t80) outliers start: 44 outliers final: 25 residues processed: 280 average time/residue: 1.0349 time to fit residues: 311.2948 Evaluate side-chains 289 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 0.0570 chunk 95 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.109651 restraints weight = 13098.247| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.94 r_work: 0.3295 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9193 Z= 0.206 Angle : 0.534 7.616 12444 Z= 0.280 Chirality : 0.041 0.192 1414 Planarity : 0.004 0.061 1558 Dihedral : 5.077 51.663 1269 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.74 % Allowed : 28.14 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1125 helix: 2.32 (0.26), residues: 408 sheet: 0.16 (0.29), residues: 299 loop : -0.47 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 251 HIS 0.005 0.001 HIS S 35 PHE 0.023 0.002 PHE R 186 TYR 0.015 0.001 TYR S 178 ARG 0.008 0.001 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 0.845 Fit side-chains REVERT: A 186 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6663 (mm-30) REVERT: A 193 ASP cc_start: 0.7963 (m-30) cc_final: 0.7748 (t0) REVERT: A 197 LYS cc_start: 0.8478 (mtmm) cc_final: 0.8273 (mtpp) REVERT: A 231 ASP cc_start: 0.7776 (t0) cc_final: 0.7472 (t0) REVERT: A 269 ASN cc_start: 0.8442 (m-40) cc_final: 0.8161 (m110) REVERT: A 318 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: A 328 ASP cc_start: 0.7808 (m-30) cc_final: 0.7579 (m-30) REVERT: A 340 THR cc_start: 0.8622 (m) cc_final: 0.8278 (t) REVERT: B 19 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7414 (mtm-85) REVERT: B 22 ARG cc_start: 0.7251 (mtt180) cc_final: 0.7048 (mtp180) REVERT: B 30 LEU cc_start: 0.7781 (tp) cc_final: 0.7502 (tt) REVERT: B 61 MET cc_start: 0.8179 (tmm) cc_final: 0.7957 (ppp) REVERT: B 76 ASP cc_start: 0.7569 (p0) cc_final: 0.7333 (p0) REVERT: B 130 GLU cc_start: 0.8164 (mp0) cc_final: 0.7757 (mp0) REVERT: B 197 ARG cc_start: 0.7853 (mpt-90) cc_final: 0.7520 (mtt-85) REVERT: B 214 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7548 (mmt180) REVERT: B 258 ASP cc_start: 0.8010 (t0) cc_final: 0.7321 (t0) REVERT: B 318 LEU cc_start: 0.8680 (tp) cc_final: 0.8300 (tp) REVERT: R 37 LEU cc_start: 0.8335 (tp) cc_final: 0.7906 (tm) REVERT: R 41 PHE cc_start: 0.7964 (m-80) cc_final: 0.7555 (m-80) REVERT: R 55 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7953 (tt) REVERT: R 95 LEU cc_start: 0.8619 (mt) cc_final: 0.8377 (mm) REVERT: R 105 MET cc_start: 0.7900 (mmm) cc_final: 0.7524 (mmm) REVERT: R 121 MET cc_start: 0.8180 (tpp) cc_final: 0.7624 (mpp) REVERT: R 168 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7715 (mp) REVERT: R 235 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7363 (mmmm) REVERT: R 298 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8263 (t) REVERT: S 69 THR cc_start: 0.8179 (p) cc_final: 0.7957 (t) REVERT: S 98 ARG cc_start: 0.8699 (ptm160) cc_final: 0.8420 (ptm160) REVERT: S 223 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7481 (t80) outliers start: 37 outliers final: 23 residues processed: 272 average time/residue: 1.1574 time to fit residues: 337.6637 Evaluate side-chains 283 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109469 restraints weight = 13098.621| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.95 r_work: 0.3294 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9193 Z= 0.191 Angle : 0.525 7.550 12444 Z= 0.276 Chirality : 0.040 0.140 1414 Planarity : 0.004 0.061 1558 Dihedral : 5.082 53.084 1269 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.54 % Allowed : 28.44 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1125 helix: 2.36 (0.26), residues: 408 sheet: 0.22 (0.29), residues: 297 loop : -0.45 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 251 HIS 0.005 0.001 HIS S 35 PHE 0.024 0.002 PHE R 216 TYR 0.015 0.001 TYR S 178 ARG 0.008 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8092.81 seconds wall clock time: 141 minutes 22.27 seconds (8482.27 seconds total)