Starting phenix.real_space_refine on Fri Sep 11 08:45:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l1u_23118/09_2026/7l1u_23118.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l1u_23118/09_2026/7l1u_23118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l1u_23118/09_2026/7l1u_23118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l1u_23118/09_2026/7l1u_23118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l1u_23118/09_2026/7l1u_23118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l1u_23118/09_2026/7l1u_23118.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7l1u_23118/09_2026/7l1u_23118.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l1u_23118/09_2026/7l1u_23118.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 63 5.16 5 C 5586 2.51 5 N 1498 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8723 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1802 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 7, 'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2496 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "C" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 422 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1719 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "R" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2220 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.99, per 1000 atoms: 0.23 Number of scatterers: 8723 At special positions: 0 Unit cell: (112.56, 108.36, 137.76, 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 63 16.00 O 1576 8.00 N 1498 7.00 C 5586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 210 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 448.8 milliseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 36.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.291A pdb=" N ARG A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.544A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.870A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.732A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.752A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.184A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.519A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 6 through 24 removed outlier: 3.764A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.594A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.572A pdb=" N ASP H 223 " --> pdb=" O GLU H 220 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 220 through 224' Processing helix chain 'R' and resid 52 through 55 Processing helix chain 'R' and resid 56 through 82 Processing helix chain 'R' and resid 89 through 107 removed outlier: 3.947A pdb=" N ILE R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 118 Processing helix chain 'R' and resid 122 through 157 removed outlier: 4.083A pdb=" N LEU R 126 " --> pdb=" O PHE R 122 " (cutoff:3.500A) Proline residue: R 131 - end of helix Processing helix chain 'R' and resid 165 through 184 removed outlier: 3.854A pdb=" N MET R 184 " --> pdb=" O SER R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 190 removed outlier: 4.025A pdb=" N VAL R 190 " --> pdb=" O PRO R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 232 removed outlier: 3.948A pdb=" N MET R 222 " --> pdb=" O ILE R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 250 Processing helix chain 'R' and resid 293 through 316 removed outlier: 4.153A pdb=" N LYS R 301 " --> pdb=" O ARG R 297 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR R 302 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA R 303 " --> pdb=" O ARG R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 328 removed outlier: 3.707A pdb=" N SER R 321 " --> pdb=" O TYR R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 364 removed outlier: 3.805A pdb=" N VAL R 342 " --> pdb=" O ASP R 338 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 376 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.270A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.792A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.017A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.083A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.600A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.508A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.677A 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: 6.712A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.444A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.523A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.545A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 194 through 195 removed outlier: 5.529A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 191 through 195 430 hydrogen bonds defined for protein. 1218 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: 1.35 Time building geometry restraints manager: 0.95 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: 2677 1.34 - 1.46: 1900 1.46 - 1.58: 4241 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 8910 Sorted by residual: bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.722 0.086 3.30e-02 9.18e+02 6.85e+00 bond pdb=" CA GLN H 142 " pdb=" CB GLN H 142 " ideal model delta sigma weight residual 1.527 1.462 0.065 2.48e-02 1.63e+03 6.83e+00 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.419 0.079 3.10e-02 1.04e+03 6.52e+00 bond pdb=" C TYR A 360 " pdb=" N PRO A 361 " ideal model delta sigma weight residual 1.334 1.307 0.027 1.11e-02 8.12e+03 6.03e+00 bond pdb=" CG LEU B 79 " pdb=" CD2 LEU B 79 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.45e+00 ... (remaining 8905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 11507 2.10 - 4.20: 542 4.20 - 6.29: 47 6.29 - 8.39: 17 8.39 - 10.49: 1 Bond angle restraints: 12114 Sorted by residual: angle pdb=" C LYS B 301 " pdb=" N ALA B 302 " pdb=" CA ALA B 302 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C PRO B 236 " pdb=" N ASN B 237 " pdb=" CA ASN B 237 " ideal model delta sigma weight residual 122.38 115.79 6.59 1.81e+00 3.05e-01 1.32e+01 angle pdb=" C VAL H 48 " pdb=" N ALA H 49 " pdb=" CA ALA H 49 " ideal model delta sigma weight residual 121.75 115.93 5.82 1.73e+00 3.34e-01 1.13e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N GLY B 282 " pdb=" CA GLY B 282 " pdb=" C GLY B 282 " ideal model delta sigma weight residual 116.01 110.71 5.30 1.64e+00 3.72e-01 1.04e+01 ... (remaining 12109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 4637 15.93 - 31.85: 498 31.85 - 47.78: 93 47.78 - 63.71: 14 63.71 - 79.64: 4 Dihedral angle restraints: 5246 sinusoidal: 1905 harmonic: 3341 Sorted by residual: dihedral pdb=" CA PHE R 121 " pdb=" C PHE R 121 " pdb=" N PHE R 122 " pdb=" CA PHE R 122 " ideal model delta harmonic sigma weight residual 180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA SER H 208 " pdb=" C SER H 208 " pdb=" N GLY H 209 " pdb=" CA GLY H 209 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ALA R 234 " pdb=" C ALA R 234 " pdb=" N PRO R 235 " pdb=" CA PRO R 235 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 5243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 878 0.050 - 0.100: 391 0.100 - 0.150: 113 0.150 - 0.200: 19 0.200 - 0.250: 8 Chirality restraints: 1409 Sorted by residual: chirality pdb=" CB VAL R 73 " pdb=" CA VAL R 73 " pdb=" CG1 VAL R 73 " pdb=" CG2 VAL R 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE H 100 " pdb=" CA ILE H 100 " pdb=" CG1 ILE H 100 " pdb=" CG2 ILE H 100 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL H 48 " pdb=" CA VAL H 48 " pdb=" CG1 VAL H 48 " pdb=" CG2 VAL H 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1406 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA R 234 " 0.050 5.00e-02 4.00e+02 7.49e-02 8.97e+00 pdb=" N PRO R 235 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 235 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 235 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO B 236 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO B 194 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.038 5.00e-02 4.00e+02 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1121 2.74 - 3.28: 7690 3.28 - 3.82: 13832 3.82 - 4.36: 15948 4.36 - 4.90: 29381 Nonbonded interactions: 67972 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.202 3.040 nonbonded pdb=" O SER A 250 " pdb=" OG SER A 250 " model vdw 2.288 3.040 nonbonded pdb=" O VAL R 114 " pdb=" OH TYR R 343 " model vdw 2.307 3.040 nonbonded pdb=" OE2 GLU A 15 " pdb=" OH TYR H 175 " model vdw 2.308 3.040 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.315 3.040 ... (remaining 67967 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: 2.470 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.260 Find NCS groups from input model: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.011 0.205 8914 Z= 0.489 Angle : 0.996 10.490 12120 Z= 0.570 Chirality : 0.062 0.250 1409 Planarity : 0.007 0.075 1518 Dihedral : 13.515 79.637 3077 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.78 % Allowed : 9.22 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.20), residues: 1128 helix: -2.10 (0.20), residues: 391 sheet: -1.25 (0.28), residues: 294 loop : -2.62 (0.23), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 72 TYR 0.037 0.003 TYR B 59 PHE 0.031 0.003 PHE B 199 TRP 0.022 0.003 TRP H 47 HIS 0.008 0.002 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.01053 / 0.44 ( 8910) covalent geometry : angle 0.99601 / 0.57 (12114) SS BOND : bond 0.01117 / 0.58 ( 3) SS BOND : angle 1.67775 / 0.71 ( 6) hydrogen bonds : bond 0.15349 / 10.19 ( 430) hydrogen bonds : angle 6.22565 / 4.41 ( 1218) Misc. bond : bond 0.20478 / 10.78 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.331 Fit side-chains REVERT: A 209 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8067 (mt-10) REVERT: B 293 ASN cc_start: 0.8425 (p0) cc_final: 0.8137 (p0) REVERT: C 47 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7554 (mp0) REVERT: H 87 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.7995 (mtt-85) REVERT: R 122 PHE cc_start: 0.6672 (m-80) cc_final: 0.6379 (m-80) REVERT: R 191 MET cc_start: 0.8699 (mmt) cc_final: 0.8118 (mmp) REVERT: R 239 MET cc_start: 0.8077 (ttm) cc_final: 0.7823 (mtp) REVERT: R 339 ARG cc_start: 0.7272 (ptm-80) cc_final: 0.6497 (ttt-90) outliers start: 7 outliers final: 5 residues processed: 155 average time/residue: 0.1152 time to fit residues: 23.5689 Evaluate side-chains 130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 100 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.4979 > 50:) chunk 106 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 88 ASN H 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.155741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116601 restraints weight = 11748.669| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.76 r_work: 0.3214 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8914 Z= 0.129 Angle : 0.563 6.315 12120 Z= 0.306 Chirality : 0.043 0.174 1409 Planarity : 0.004 0.055 1518 Dihedral : 5.172 37.022 1246 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.11 % Allowed : 13.56 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.23), residues: 1128 helix: 0.23 (0.25), residues: 391 sheet: -0.51 (0.30), residues: 265 loop : -2.14 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 22 TYR 0.017 0.001 TYR H 190 PHE 0.012 0.001 PHE A 212 TRP 0.013 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8910) covalent geometry : angle 0.56330 / 0.31 (12114) SS BOND : bond 0.00419 / 0.21 ( 3) SS BOND : angle 0.75757 / 0.36 ( 6) hydrogen bonds : bond 0.04650 / 3.16 ( 430) hydrogen bonds : angle 4.73370 / 3.38 ( 1218) Misc. bond : bond 0.00076 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.321 Fit side-chains REVERT: A 209 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8228 (mt-10) REVERT: A 385 GLN cc_start: 0.7857 (tp40) cc_final: 0.7551 (tp40) REVERT: B 76 ASP cc_start: 0.8978 (p0) cc_final: 0.8589 (p0) REVERT: B 130 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8546 (mt-10) REVERT: B 293 ASN cc_start: 0.8257 (p0) cc_final: 0.7962 (p0) REVERT: C 47 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7645 (mp0) REVERT: H 71 SER cc_start: 0.7801 (t) cc_final: 0.7373 (p) REVERT: R 122 PHE cc_start: 0.6774 (m-80) cc_final: 0.6393 (m-80) REVERT: R 191 MET cc_start: 0.8836 (mmt) cc_final: 0.8573 (mmp) REVERT: R 339 ARG cc_start: 0.7246 (ptm-80) cc_final: 0.6728 (ttt180) outliers start: 19 outliers final: 16 residues processed: 151 average time/residue: 0.0912 time to fit residues: 19.0740 Evaluate side-chains 139 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.155565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116765 restraints weight = 11565.552| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.71 r_work: 0.3218 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8914 Z= 0.129 Angle : 0.532 5.809 12120 Z= 0.287 Chirality : 0.042 0.144 1409 Planarity : 0.004 0.045 1518 Dihedral : 4.801 37.217 1244 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.67 % Allowed : 14.89 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.25), residues: 1128 helix: 1.18 (0.27), residues: 392 sheet: -0.19 (0.30), residues: 263 loop : -1.83 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 304 TYR 0.017 0.001 TYR H 190 PHE 0.013 0.001 PHE A 212 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 8910) covalent geometry : angle 0.53226 / 0.29 (12114) SS BOND : bond 0.00437 / 0.23 ( 3) SS BOND : angle 0.60864 / 0.30 ( 6) hydrogen bonds : bond 0.04144 / 2.81 ( 430) hydrogen bonds : angle 4.49018 / 3.21 ( 1218) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.296 Fit side-chains REVERT: B 76 ASP cc_start: 0.8950 (p0) cc_final: 0.8574 (p0) REVERT: B 130 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8479 (mt-10) REVERT: B 293 ASN cc_start: 0.8240 (p0) cc_final: 0.8002 (p0) REVERT: C 47 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7604 (mp0) REVERT: H 71 SER cc_start: 0.7799 (t) cc_final: 0.7390 (p) REVERT: H 87 ARG cc_start: 0.8408 (mtt-85) cc_final: 0.8130 (mtt-85) REVERT: R 122 PHE cc_start: 0.6754 (m-80) cc_final: 0.6420 (m-80) REVERT: R 191 MET cc_start: 0.8837 (mmt) cc_final: 0.8535 (mmp) outliers start: 24 outliers final: 20 residues processed: 144 average time/residue: 0.0939 time to fit residues: 19.0519 Evaluate side-chains 148 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.153124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114142 restraints weight = 11822.405| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.72 r_work: 0.3184 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8914 Z= 0.190 Angle : 0.567 5.997 12120 Z= 0.306 Chirality : 0.044 0.167 1409 Planarity : 0.004 0.043 1518 Dihedral : 4.963 38.755 1244 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.67 % Allowed : 15.11 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1128 helix: 1.52 (0.27), residues: 392 sheet: -0.34 (0.30), residues: 269 loop : -1.67 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 304 TYR 0.019 0.001 TYR H 190 PHE 0.015 0.002 PHE B 199 TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 ( 8910) covalent geometry : angle 0.56664 / 0.31 (12114) SS BOND : bond 0.00527 / 0.28 ( 3) SS BOND : angle 0.66519 / 0.33 ( 6) hydrogen bonds : bond 0.04533 / 3.08 ( 430) hydrogen bonds : angle 4.51406 / 3.21 ( 1218) Misc. bond : bond 0.00030 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.336 Fit side-chains REVERT: A 209 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8135 (mt-10) REVERT: A 285 ILE cc_start: 0.9102 (mm) cc_final: 0.8868 (mm) REVERT: B 76 ASP cc_start: 0.9021 (p0) cc_final: 0.8660 (p0) REVERT: B 130 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8492 (mt-10) REVERT: B 293 ASN cc_start: 0.8294 (p0) cc_final: 0.7993 (p0) REVERT: C 47 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7565 (mp0) REVERT: H 71 SER cc_start: 0.7886 (OUTLIER) cc_final: 0.7418 (p) REVERT: R 122 PHE cc_start: 0.6734 (m-80) cc_final: 0.6332 (m-80) REVERT: R 191 MET cc_start: 0.8802 (mmt) cc_final: 0.8426 (mmp) outliers start: 33 outliers final: 25 residues processed: 153 average time/residue: 0.0897 time to fit residues: 19.4979 Evaluate side-chains 155 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.159328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118796 restraints weight = 11819.530| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.83 r_work: 0.3419 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8914 Z= 0.125 Angle : 0.519 5.798 12120 Z= 0.278 Chirality : 0.042 0.142 1409 Planarity : 0.003 0.042 1518 Dihedral : 4.659 37.219 1244 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.33 % Allowed : 16.56 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 1128 helix: 1.86 (0.27), residues: 386 sheet: -0.23 (0.31), residues: 260 loop : -1.52 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 304 TYR 0.016 0.001 TYR H 190 PHE 0.012 0.001 PHE A 212 TRP 0.010 0.001 TRP R 351 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 8910) covalent geometry : angle 0.51929 / 0.28 (12114) SS BOND : bond 0.00420 / 0.22 ( 3) SS BOND : angle 0.55810 / 0.29 ( 6) hydrogen bonds : bond 0.03886 / 2.64 ( 430) hydrogen bonds : angle 4.32398 / 3.09 ( 1218) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.310 Fit side-chains REVERT: B 130 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8494 (mt-10) REVERT: B 293 ASN cc_start: 0.8299 (p0) cc_final: 0.8056 (p0) REVERT: H 71 SER cc_start: 0.7738 (OUTLIER) cc_final: 0.7363 (p) REVERT: R 122 PHE cc_start: 0.6723 (m-80) cc_final: 0.6361 (m-80) REVERT: R 151 ASP cc_start: 0.8503 (t70) cc_final: 0.7782 (t0) REVERT: R 191 MET cc_start: 0.8756 (mmt) cc_final: 0.8273 (mmp) outliers start: 30 outliers final: 22 residues processed: 159 average time/residue: 0.0862 time to fit residues: 19.5682 Evaluate side-chains 156 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.160580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120189 restraints weight = 11890.566| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.84 r_work: 0.3489 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8914 Z= 0.108 Angle : 0.507 6.709 12120 Z= 0.271 Chirality : 0.042 0.142 1409 Planarity : 0.003 0.041 1518 Dihedral : 4.438 36.904 1244 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.44 % Allowed : 17.33 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1128 helix: 2.03 (0.27), residues: 386 sheet: -0.10 (0.30), residues: 262 loop : -1.41 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 304 TYR 0.016 0.001 TYR H 190 PHE 0.011 0.001 PHE A 212 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8910) covalent geometry : angle 0.50689 / 0.27 (12114) SS BOND : bond 0.00380 / 0.20 ( 3) SS BOND : angle 0.49726 / 0.26 ( 6) hydrogen bonds : bond 0.03627 / 2.47 ( 430) hydrogen bonds : angle 4.21175 / 3.00 ( 1218) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.343 Fit side-chains REVERT: H 71 SER cc_start: 0.7693 (OUTLIER) cc_final: 0.7299 (p) REVERT: R 122 PHE cc_start: 0.6730 (m-80) cc_final: 0.6382 (m-80) REVERT: R 151 ASP cc_start: 0.8443 (t70) cc_final: 0.7721 (t0) REVERT: R 184 MET cc_start: 0.8266 (mmt) cc_final: 0.7344 (mtp) REVERT: R 191 MET cc_start: 0.8740 (mmt) cc_final: 0.8266 (mmp) outliers start: 31 outliers final: 25 residues processed: 152 average time/residue: 0.0872 time to fit residues: 18.9442 Evaluate side-chains 159 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 0.3980 chunk 24 optimal weight: 0.0020 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.0470 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.162389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122362 restraints weight = 11906.354| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.83 r_work: 0.3513 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8914 Z= 0.096 Angle : 0.514 8.164 12120 Z= 0.269 Chirality : 0.041 0.141 1409 Planarity : 0.003 0.041 1518 Dihedral : 4.204 36.018 1244 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.89 % Allowed : 18.89 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1128 helix: 2.12 (0.27), residues: 386 sheet: 0.02 (0.30), residues: 258 loop : -1.35 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 304 TYR 0.015 0.001 TYR H 190 PHE 0.011 0.001 PHE A 212 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 ( 8910) covalent geometry : angle 0.51433 / 0.27 (12114) SS BOND : bond 0.00352 / 0.18 ( 3) SS BOND : angle 0.45825 / 0.24 ( 6) hydrogen bonds : bond 0.03369 / 2.29 ( 430) hydrogen bonds : angle 4.10614 / 2.92 ( 1218) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.213 Fit side-chains REVERT: H 71 SER cc_start: 0.7725 (OUTLIER) cc_final: 0.7326 (p) REVERT: R 98 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7365 (mp) REVERT: R 122 PHE cc_start: 0.6667 (m-80) cc_final: 0.6322 (m-80) REVERT: R 151 ASP cc_start: 0.8428 (t70) cc_final: 0.7729 (t0) REVERT: R 191 MET cc_start: 0.8666 (mmt) cc_final: 0.7817 (mmp) REVERT: R 339 ARG cc_start: 0.7151 (ptm-80) cc_final: 0.6579 (ttt180) outliers start: 26 outliers final: 23 residues processed: 152 average time/residue: 0.0852 time to fit residues: 18.3162 Evaluate side-chains 154 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN B 75 GLN R 245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115034 restraints weight = 11722.604| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.71 r_work: 0.3200 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8914 Z= 0.188 Angle : 0.582 9.134 12120 Z= 0.307 Chirality : 0.044 0.166 1409 Planarity : 0.004 0.044 1518 Dihedral : 4.587 36.979 1244 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.00 % Allowed : 18.67 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.25), residues: 1128 helix: 1.99 (0.27), residues: 386 sheet: -0.22 (0.31), residues: 261 loop : -1.29 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 304 TYR 0.019 0.001 TYR H 190 PHE 0.015 0.002 PHE B 199 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 8910) covalent geometry : angle 0.58198 / 0.31 (12114) SS BOND : bond 0.00541 / 0.28 ( 3) SS BOND : angle 0.62805 / 0.31 ( 6) hydrogen bonds : bond 0.04253 / 2.89 ( 430) hydrogen bonds : angle 4.28810 / 3.05 ( 1218) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.326 Fit side-chains REVERT: A 209 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8252 (mt-10) REVERT: B 59 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: B 273 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8447 (mp) REVERT: H 71 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7414 (p) REVERT: R 98 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7300 (mp) REVERT: R 122 PHE cc_start: 0.6728 (m-80) cc_final: 0.6336 (m-80) REVERT: R 184 MET cc_start: 0.8263 (mmt) cc_final: 0.7279 (mtp) REVERT: R 191 MET cc_start: 0.8711 (mmt) cc_final: 0.8143 (mmp) outliers start: 36 outliers final: 28 residues processed: 145 average time/residue: 0.0883 time to fit residues: 18.1316 Evaluate side-chains 156 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.160912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120811 restraints weight = 11844.061| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.82 r_work: 0.3507 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8914 Z= 0.107 Angle : 0.529 8.091 12120 Z= 0.278 Chirality : 0.042 0.139 1409 Planarity : 0.003 0.048 1518 Dihedral : 4.343 36.884 1244 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.11 % Allowed : 19.78 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1128 helix: 2.11 (0.27), residues: 386 sheet: -0.12 (0.30), residues: 265 loop : -1.24 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 304 TYR 0.015 0.001 TYR H 190 PHE 0.012 0.001 PHE A 212 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 8910) covalent geometry : angle 0.52927 / 0.28 (12114) SS BOND : bond 0.00387 / 0.20 ( 3) SS BOND : angle 0.54273 / 0.29 ( 6) hydrogen bonds : bond 0.03632 / 2.47 ( 430) hydrogen bonds : angle 4.15545 / 2.96 ( 1218) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.356 Fit side-chains REVERT: B 59 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.8322 (m-80) REVERT: H 71 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.7413 (p) REVERT: H 223 ASP cc_start: 0.8456 (m-30) cc_final: 0.8247 (m-30) REVERT: R 98 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7497 (mp) REVERT: R 122 PHE cc_start: 0.6723 (m-80) cc_final: 0.6322 (m-80) REVERT: R 151 ASP cc_start: 0.8589 (t70) cc_final: 0.7911 (t0) REVERT: R 184 MET cc_start: 0.8250 (mmt) cc_final: 0.7346 (mtp) REVERT: R 191 MET cc_start: 0.8788 (mmt) cc_final: 0.8258 (mmp) outliers start: 28 outliers final: 24 residues processed: 144 average time/residue: 0.0894 time to fit residues: 18.1111 Evaluate side-chains 157 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 0.0030 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 0.0870 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.5168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115092 restraints weight = 11588.137| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.68 r_work: 0.3530 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8914 Z= 0.104 Angle : 0.527 9.156 12120 Z= 0.276 Chirality : 0.042 0.146 1409 Planarity : 0.003 0.052 1518 Dihedral : 4.195 36.012 1244 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.78 % Allowed : 20.56 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.25), residues: 1128 helix: 2.08 (0.27), residues: 392 sheet: 0.00 (0.30), residues: 264 loop : -1.17 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 304 TYR 0.015 0.001 TYR H 190 PHE 0.011 0.001 PHE A 212 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 8910) covalent geometry : angle 0.52695 / 0.28 (12114) SS BOND : bond 0.00385 / 0.20 ( 3) SS BOND : angle 0.46213 / 0.24 ( 6) hydrogen bonds : bond 0.03464 / 2.35 ( 430) hydrogen bonds : angle 4.08648 / 2.91 ( 1218) Misc. bond : bond 0.00012 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.357 Fit side-chains REVERT: B 59 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: H 71 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7446 (p) REVERT: H 223 ASP cc_start: 0.8337 (m-30) cc_final: 0.8125 (m-30) REVERT: R 98 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7491 (mp) REVERT: R 122 PHE cc_start: 0.6715 (m-80) cc_final: 0.6293 (m-80) REVERT: R 151 ASP cc_start: 0.8593 (t70) cc_final: 0.7930 (t0) REVERT: R 184 MET cc_start: 0.8228 (mmt) cc_final: 0.7325 (mtp) REVERT: R 191 MET cc_start: 0.8804 (mmt) cc_final: 0.8280 (mmp) outliers start: 25 outliers final: 22 residues processed: 145 average time/residue: 0.0960 time to fit residues: 19.5193 Evaluate side-chains 155 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 111 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 118 GLU Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 251 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 93 optimal weight: 0.0970 chunk 45 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN R 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.156648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118604 restraints weight = 11591.412| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.63 r_work: 0.3518 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8914 Z= 0.122 Angle : 0.544 9.875 12120 Z= 0.283 Chirality : 0.042 0.143 1409 Planarity : 0.003 0.054 1518 Dihedral : 4.194 35.984 1243 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.11 % Allowed : 20.11 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.25), residues: 1128 helix: 2.17 (0.27), residues: 386 sheet: 0.05 (0.30), residues: 264 loop : -1.14 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 304 TYR 0.016 0.001 TYR H 190 PHE 0.012 0.001 PHE A 212 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8910) covalent geometry : angle 0.54381 / 0.28 (12114) SS BOND : bond 0.00419 / 0.22 ( 3) SS BOND : angle 0.50185 / 0.26 ( 6) hydrogen bonds : bond 0.03615 / 2.46 ( 430) hydrogen bonds : angle 4.07824 / 2.90 ( 1218) Misc. bond : bond 0.00018 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2280.98 seconds wall clock time: 39 minutes 49.21 seconds (2389.21 seconds total)