Starting phenix.real_space_refine on Tue Mar 3 14:59:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lwc_63440/03_2026/9lwc_63440.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lwc_63440/03_2026/9lwc_63440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lwc_63440/03_2026/9lwc_63440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lwc_63440/03_2026/9lwc_63440.map" model { file = "/net/cci-nas-00/data/ceres_data/9lwc_63440/03_2026/9lwc_63440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lwc_63440/03_2026/9lwc_63440.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.091 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 43 5.16 5 C 4020 2.51 5 N 1078 2.21 5 O 1095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6236 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1413 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 188} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 8, 'GLN:plan1': 6, 'ASP:plan': 11, 'ASN:plan1': 3, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 154 Chain: "B" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2104 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 286} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 6, 'GLN:plan1': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 83 Chain: "G" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 160 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 675 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1871 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 9, 'PHE:plan': 8, 'GLU:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'ALE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.48, per 1000 atoms: 0.24 Number of scatterers: 6236 At special positions: 0 Unit cell: (70.3625, 92.0125, 121.24, 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 43 16.00 O 1095 8.00 N 1078 7.00 C 4020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " 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: 0.55 Conformation dependent library (CDL) restraints added in 414.2 milliseconds 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1636 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 10 sheets defined 41.3% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 18 through 40 removed outlier: 3.688A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.921A pdb=" N LYS A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.523A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.545A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'G' and resid 32 through 44 removed outlier: 3.671A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 23 through 51 Processing helix chain 'R' and resid 58 through 88 removed outlier: 4.136A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 97 through 127 removed outlier: 3.586A pdb=" N VAL R 107 " --> pdb=" O ASP R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 161 removed outlier: 3.646A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix removed outlier: 3.904A pdb=" N LEU R 161 " --> pdb=" O ILE R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 238 removed outlier: 5.148A pdb=" N ILE R 205 " --> pdb=" O ILE R 201 " (cutoff:3.500A) Proline residue: R 206 - end of helix removed outlier: 3.579A pdb=" N LEU R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA R 238 " --> pdb=" O ALA R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 295 removed outlier: 3.660A pdb=" N ILE R 277 " --> pdb=" O THR R 273 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 315 through 320 Processing helix chain 'R' and resid 322 through 332 removed outlier: 3.846A pdb=" N LEU R 326 " --> pdb=" O ALA R 322 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 336 through 343 removed outlier: 3.571A pdb=" N ALA R 340 " --> pdb=" O ASP R 336 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR R 343 " --> pdb=" O LYS R 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 222 removed outlier: 6.974A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 5.794A 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: 4.072A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.695A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.550A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.727A 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 153 removed outlier: 6.819A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.602A 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 193 removed outlier: 3.612A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU B 198 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.576A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.603A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 297 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 6 through 7 removed outlier: 3.517A pdb=" N SER N 7 " --> pdb=" O SER N 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 34 through 39 removed outlier: 3.518A pdb=" N VAL N 37 " --> pdb=" O TYR N 95 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 918 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: 0.99 Time building geometry restraints manager: 0.76 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: 1977 1.34 - 1.46: 1073 1.46 - 1.58: 3243 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6353 Sorted by residual: bond pdb=" C1 ALE R 501 " pdb=" C2 ALE R 501 " ideal model delta sigma weight residual 1.392 1.514 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C5 ALE R 501 " pdb=" C6 ALE R 501 " ideal model delta sigma weight residual 1.389 1.503 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C3 ALE R 501 " pdb=" C4 ALE R 501 " ideal model delta sigma weight residual 1.400 1.502 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C2 ALE R 501 " pdb=" C3 ALE R 501 " ideal model delta sigma weight residual 1.386 1.288 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C4 ALE R 501 " pdb=" C5 ALE R 501 " ideal model delta sigma weight residual 1.386 1.294 0.092 2.00e-02 2.50e+03 2.10e+01 ... (remaining 6348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 8417 1.75 - 3.50: 183 3.50 - 5.24: 48 5.24 - 6.99: 3 6.99 - 8.74: 6 Bond angle restraints: 8657 Sorted by residual: angle pdb=" N TRP R 318 " pdb=" CA TRP R 318 " pdb=" C TRP R 318 " ideal model delta sigma weight residual 114.31 109.18 5.13 1.29e+00 6.01e-01 1.58e+01 angle pdb=" N VAL G 30 " pdb=" CA VAL G 30 " pdb=" C VAL G 30 " ideal model delta sigma weight residual 106.21 110.33 -4.12 1.07e+00 8.73e-01 1.48e+01 angle pdb=" N THR B 196 " pdb=" CA THR B 196 " pdb=" C THR B 196 " ideal model delta sigma weight residual 111.90 106.95 4.95 1.32e+00 5.74e-01 1.41e+01 angle pdb=" N GLY B 216 " pdb=" CA GLY B 216 " pdb=" C GLY B 216 " ideal model delta sigma weight residual 113.18 121.92 -8.74 2.37e+00 1.78e-01 1.36e+01 angle pdb=" N PHE R 337 " pdb=" CA PHE R 337 " pdb=" C PHE R 337 " ideal model delta sigma weight residual 112.90 108.10 4.80 1.31e+00 5.83e-01 1.34e+01 ... (remaining 8652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.87: 3257 19.87 - 39.73: 304 39.73 - 59.59: 98 59.59 - 79.46: 12 79.46 - 99.32: 5 Dihedral angle restraints: 3676 sinusoidal: 1170 harmonic: 2506 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -125.53 39.53 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual 180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PHE R 203 " pdb=" C PHE R 203 " pdb=" N TYR R 204 " pdb=" CA TYR R 204 " ideal model delta harmonic sigma weight residual 180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 3673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 941 0.076 - 0.153: 90 0.153 - 0.229: 5 0.229 - 0.306: 3 0.306 - 0.382: 1 Chirality restraints: 1040 Sorted by residual: chirality pdb=" C7 ALE R 501 " pdb=" C1 ALE R 501 " pdb=" C8 ALE R 501 " pdb=" O3 ALE R 501 " both_signs ideal model delta sigma weight residual False 2.28 1.90 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA THR B 181 " pdb=" N THR B 181 " pdb=" C THR B 181 " pdb=" CB THR B 181 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA LYS A 53 " pdb=" N LYS A 53 " pdb=" C LYS A 53 " pdb=" CB LYS A 53 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1037 not shown) Planarity restraints: 1077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 315 " 0.016 2.00e-02 2.50e+03 3.09e-02 9.55e+00 pdb=" C VAL R 315 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL R 315 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE R 316 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 ALE R 501 " 0.029 2.00e-02 2.50e+03 1.79e-02 7.19e+00 pdb=" C2 ALE R 501 " 0.011 2.00e-02 2.50e+03 pdb=" C3 ALE R 501 " -0.006 2.00e-02 2.50e+03 pdb=" C4 ALE R 501 " -0.008 2.00e-02 2.50e+03 pdb=" C5 ALE R 501 " 0.001 2.00e-02 2.50e+03 pdb=" C6 ALE R 501 " 0.018 2.00e-02 2.50e+03 pdb=" C7 ALE R 501 " -0.036 2.00e-02 2.50e+03 pdb=" O1 ALE R 501 " 0.006 2.00e-02 2.50e+03 pdb=" O2 ALE R 501 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 314 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C ILE R 314 " -0.037 2.00e-02 2.50e+03 pdb=" O ILE R 314 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL R 315 " 0.012 2.00e-02 2.50e+03 ... (remaining 1074 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 718 2.75 - 3.29: 5892 3.29 - 3.82: 10428 3.82 - 4.36: 12162 4.36 - 4.90: 21468 Nonbonded interactions: 50668 Sorted by model distance: nonbonded pdb=" OG1 THR R 108 " pdb=" OG SER R 202 " model vdw 2.210 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.230 3.120 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.258 3.120 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.261 3.120 nonbonded pdb=" NH1 ARG N 38 " pdb=" OH TYR N 94 " model vdw 2.285 3.120 ... (remaining 50663 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: 3.230 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 6356 Z= 0.252 Angle : 0.676 8.742 8663 Z= 0.401 Chirality : 0.049 0.382 1040 Planarity : 0.004 0.037 1077 Dihedral : 17.748 99.324 2031 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.71 % Allowed : 28.57 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.30), residues: 821 helix: 1.76 (0.29), residues: 316 sheet: -1.57 (0.33), residues: 213 loop : -1.67 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.012 0.001 TYR R 194 PHE 0.013 0.001 PHE R 288 TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 6353) covalent geometry : angle 0.67575 ( 8657) SS BOND : bond 0.00220 ( 3) SS BOND : angle 0.98883 ( 6) hydrogen bonds : bond 0.18343 ( 320) hydrogen bonds : angle 6.72758 ( 918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.279 Fit side-chains outliers start: 32 outliers final: 28 residues processed: 98 average time/residue: 0.4226 time to fit residues: 44.0670 Evaluate side-chains 94 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 53 HIS Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 225 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 77 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN R 317 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151089 restraints weight = 7669.763| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.37 r_work: 0.3613 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6356 Z= 0.137 Angle : 0.522 6.756 8663 Z= 0.285 Chirality : 0.042 0.150 1040 Planarity : 0.003 0.033 1077 Dihedral : 9.235 76.236 959 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 7.50 % Allowed : 22.86 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.29), residues: 821 helix: 2.07 (0.29), residues: 316 sheet: -1.44 (0.34), residues: 202 loop : -1.69 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 118 TYR 0.012 0.001 TYR R 194 PHE 0.018 0.001 PHE R 288 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6353) covalent geometry : angle 0.52199 ( 8657) SS BOND : bond 0.00191 ( 3) SS BOND : angle 0.90257 ( 6) hydrogen bonds : bond 0.04549 ( 320) hydrogen bonds : angle 4.84692 ( 918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 76 time to evaluate : 0.297 Fit side-chains REVERT: A 386 MET cc_start: 0.7748 (tmm) cc_final: 0.7401 (tmt) REVERT: B 118 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8012 (p0) REVERT: B 192 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8181 (mt) REVERT: R 23 ARG cc_start: 0.6358 (OUTLIER) cc_final: 0.5020 (mtp180) outliers start: 42 outliers final: 24 residues processed: 112 average time/residue: 0.4582 time to fit residues: 54.2394 Evaluate side-chains 98 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 53 HIS Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 237 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 77 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.167851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.149132 restraints weight = 7644.948| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.38 r_work: 0.3617 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6356 Z= 0.150 Angle : 0.515 5.481 8663 Z= 0.281 Chirality : 0.042 0.144 1040 Planarity : 0.003 0.033 1077 Dihedral : 8.049 58.493 940 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 7.14 % Allowed : 23.04 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.29), residues: 821 helix: 2.13 (0.29), residues: 318 sheet: -1.46 (0.34), residues: 205 loop : -1.63 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.013 0.001 TYR R 194 PHE 0.015 0.001 PHE R 288 TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6353) covalent geometry : angle 0.51493 ( 8657) SS BOND : bond 0.00220 ( 3) SS BOND : angle 0.99367 ( 6) hydrogen bonds : bond 0.04528 ( 320) hydrogen bonds : angle 4.60228 ( 918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 77 time to evaluate : 0.230 Fit side-chains REVERT: A 386 MET cc_start: 0.7768 (tmm) cc_final: 0.7451 (tmt) REVERT: B 49 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7203 (tpp-160) REVERT: B 118 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8072 (p0) REVERT: R 23 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.5247 (mtp180) REVERT: R 76 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6615 (mp) REVERT: R 103 ASP cc_start: 0.8868 (t0) cc_final: 0.8519 (t70) outliers start: 40 outliers final: 22 residues processed: 110 average time/residue: 0.3705 time to fit residues: 43.5750 Evaluate side-chains 100 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 53 HIS Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 225 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 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 176 GLN N 77 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.167939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.149079 restraints weight = 7706.326| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.41 r_work: 0.3630 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6356 Z= 0.141 Angle : 0.507 5.530 8663 Z= 0.274 Chirality : 0.042 0.139 1040 Planarity : 0.003 0.031 1077 Dihedral : 7.634 59.851 939 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.79 % Allowed : 24.29 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.29), residues: 821 helix: 2.17 (0.29), residues: 318 sheet: -1.45 (0.34), residues: 210 loop : -1.55 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 347 TYR 0.012 0.001 TYR R 194 PHE 0.015 0.001 PHE R 288 TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6353) covalent geometry : angle 0.50600 ( 8657) SS BOND : bond 0.00393 ( 3) SS BOND : angle 0.99458 ( 6) hydrogen bonds : bond 0.04332 ( 320) hydrogen bonds : angle 4.45932 ( 918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.235 Fit side-chains REVERT: A 247 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7728 (t) REVERT: A 386 MET cc_start: 0.7794 (tmm) cc_final: 0.7461 (tmt) REVERT: B 118 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8077 (p0) REVERT: G 42 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.5979 (pt0) REVERT: R 23 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5196 (mtp180) REVERT: R 76 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6562 (mp) REVERT: R 103 ASP cc_start: 0.8881 (t0) cc_final: 0.8645 (t0) outliers start: 38 outliers final: 23 residues processed: 104 average time/residue: 0.4040 time to fit residues: 44.7544 Evaluate side-chains 100 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 53 HIS Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 225 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 77 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.166352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147497 restraints weight = 7915.985| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.41 r_work: 0.3569 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6356 Z= 0.147 Angle : 0.508 5.380 8663 Z= 0.277 Chirality : 0.042 0.159 1040 Planarity : 0.003 0.030 1077 Dihedral : 7.435 58.943 931 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 6.79 % Allowed : 24.29 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.29), residues: 821 helix: 2.15 (0.29), residues: 318 sheet: -1.40 (0.34), residues: 210 loop : -1.60 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.012 0.001 TYR R 194 PHE 0.016 0.001 PHE R 288 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6353) covalent geometry : angle 0.50773 ( 8657) SS BOND : bond 0.00210 ( 3) SS BOND : angle 0.99999 ( 6) hydrogen bonds : bond 0.04365 ( 320) hydrogen bonds : angle 4.43497 ( 918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 0.186 Fit side-chains REVERT: A 247 VAL cc_start: 0.7947 (OUTLIER) cc_final: 0.7724 (t) REVERT: A 344 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7961 (tp30) REVERT: A 386 MET cc_start: 0.7772 (tmm) cc_final: 0.7424 (tmt) REVERT: B 118 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8152 (p0) REVERT: G 42 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5990 (pt0) REVERT: R 23 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5050 (mtp180) REVERT: R 76 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6619 (mp) outliers start: 38 outliers final: 23 residues processed: 107 average time/residue: 0.3953 time to fit residues: 45.0783 Evaluate side-chains 103 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 53 HIS Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 193 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 61 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 77 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.164571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.145818 restraints weight = 7919.120| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.40 r_work: 0.3591 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6356 Z= 0.177 Angle : 0.543 5.635 8663 Z= 0.295 Chirality : 0.043 0.140 1040 Planarity : 0.004 0.030 1077 Dihedral : 7.566 57.768 929 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 7.14 % Allowed : 23.93 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.29), residues: 821 helix: 2.04 (0.29), residues: 320 sheet: -1.40 (0.34), residues: 204 loop : -1.62 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.013 0.002 TYR R 194 PHE 0.017 0.002 PHE R 288 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 6353) covalent geometry : angle 0.54222 ( 8657) SS BOND : bond 0.00323 ( 3) SS BOND : angle 1.18668 ( 6) hydrogen bonds : bond 0.04685 ( 320) hydrogen bonds : angle 4.51837 ( 918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 0.194 Fit side-chains REVERT: A 247 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7769 (t) REVERT: A 386 MET cc_start: 0.7795 (tmm) cc_final: 0.7460 (tmt) REVERT: B 118 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8173 (p0) REVERT: G 42 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6066 (pt0) REVERT: R 23 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5120 (mtp180) REVERT: R 76 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6561 (mp) REVERT: R 216 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7859 (mtt180) outliers start: 40 outliers final: 27 residues processed: 107 average time/residue: 0.3809 time to fit residues: 43.5130 Evaluate side-chains 104 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 53 HIS Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 216 ARG Chi-restraints excluded: chain R residue 225 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.165938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147184 restraints weight = 7873.535| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.39 r_work: 0.3608 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6356 Z= 0.139 Angle : 0.506 5.235 8663 Z= 0.276 Chirality : 0.042 0.141 1040 Planarity : 0.003 0.030 1077 Dihedral : 7.282 56.535 929 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 6.61 % Allowed : 24.29 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.29), residues: 821 helix: 2.17 (0.29), residues: 316 sheet: -1.35 (0.34), residues: 204 loop : -1.59 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 347 TYR 0.012 0.001 TYR R 194 PHE 0.016 0.001 PHE R 288 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6353) covalent geometry : angle 0.50556 ( 8657) SS BOND : bond 0.00241 ( 3) SS BOND : angle 1.03336 ( 6) hydrogen bonds : bond 0.04316 ( 320) hydrogen bonds : angle 4.42093 ( 918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.248 Fit side-chains REVERT: A 247 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7757 (t) REVERT: A 386 MET cc_start: 0.7781 (tmm) cc_final: 0.7454 (tmt) REVERT: B 118 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8130 (p0) REVERT: G 42 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6071 (pt0) REVERT: R 23 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5157 (mtp180) REVERT: R 76 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6541 (mp) outliers start: 37 outliers final: 25 residues processed: 102 average time/residue: 0.4062 time to fit residues: 44.2443 Evaluate side-chains 100 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 53 HIS Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 225 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 52 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN ** R 41 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 = 0.3882 r_free = 0.3882 target = 0.166651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147864 restraints weight = 7877.515| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.40 r_work: 0.3606 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6356 Z= 0.157 Angle : 0.532 7.895 8663 Z= 0.286 Chirality : 0.042 0.144 1040 Planarity : 0.003 0.030 1077 Dihedral : 7.317 55.535 929 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.43 % Allowed : 24.82 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.29), residues: 821 helix: 2.10 (0.29), residues: 317 sheet: -1.38 (0.34), residues: 204 loop : -1.59 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 347 TYR 0.023 0.002 TYR R 321 PHE 0.017 0.001 PHE R 288 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6353) covalent geometry : angle 0.53095 ( 8657) SS BOND : bond 0.00247 ( 3) SS BOND : angle 1.13742 ( 6) hydrogen bonds : bond 0.04461 ( 320) hydrogen bonds : angle 4.45428 ( 918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 72 time to evaluate : 0.221 Fit side-chains REVERT: A 247 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7784 (t) REVERT: A 386 MET cc_start: 0.7797 (tmm) cc_final: 0.7461 (tmt) REVERT: B 118 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8184 (p0) REVERT: G 42 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6139 (pt0) REVERT: R 23 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.5116 (mtp180) REVERT: R 76 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6445 (mp) outliers start: 36 outliers final: 26 residues processed: 101 average time/residue: 0.3794 time to fit residues: 40.8754 Evaluate side-chains 101 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 53 HIS Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 225 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 25 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 113 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 = 0.4044 r_free = 0.4044 target = 0.177017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.159076 restraints weight = 7819.223| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.33 r_work: 0.3765 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6356 Z= 0.175 Angle : 0.551 7.611 8663 Z= 0.297 Chirality : 0.043 0.147 1040 Planarity : 0.004 0.032 1077 Dihedral : 7.420 55.444 929 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 6.25 % Allowed : 25.18 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.29), residues: 821 helix: 1.98 (0.29), residues: 317 sheet: -1.42 (0.34), residues: 204 loop : -1.62 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 347 TYR 0.023 0.002 TYR R 321 PHE 0.018 0.002 PHE R 288 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6353) covalent geometry : angle 0.55040 ( 8657) SS BOND : bond 0.00285 ( 3) SS BOND : angle 1.20680 ( 6) hydrogen bonds : bond 0.04639 ( 320) hydrogen bonds : angle 4.52928 ( 918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.236 Fit side-chains REVERT: A 247 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7811 (t) REVERT: A 386 MET cc_start: 0.7779 (tmm) cc_final: 0.7433 (tmt) REVERT: B 118 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8199 (p0) REVERT: G 42 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6371 (pt0) REVERT: R 23 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.5065 (mtp180) REVERT: R 76 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6341 (mp) REVERT: R 216 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7893 (mtt180) outliers start: 35 outliers final: 26 residues processed: 104 average time/residue: 0.3867 time to fit residues: 43.0852 Evaluate side-chains 104 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 53 HIS Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 216 ARG Chi-restraints excluded: chain R residue 225 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.176774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.159138 restraints weight = 7802.303| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.29 r_work: 0.3788 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6356 Z= 0.139 Angle : 0.515 7.588 8663 Z= 0.277 Chirality : 0.042 0.144 1040 Planarity : 0.003 0.032 1077 Dihedral : 7.125 54.501 929 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.71 % Allowed : 25.36 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.29), residues: 821 helix: 2.03 (0.29), residues: 315 sheet: -1.31 (0.34), residues: 204 loop : -1.57 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.019 0.001 TYR R 321 PHE 0.017 0.001 PHE R 288 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6353) covalent geometry : angle 0.51458 ( 8657) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.91686 ( 6) hydrogen bonds : bond 0.04284 ( 320) hydrogen bonds : angle 4.41934 ( 918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.235 Fit side-chains REVERT: A 247 VAL cc_start: 0.8088 (OUTLIER) cc_final: 0.7820 (t) REVERT: A 386 MET cc_start: 0.7775 (tmm) cc_final: 0.7444 (tmt) REVERT: B 118 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8156 (p0) REVERT: G 42 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6436 (pt0) REVERT: R 23 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5091 (mtp180) REVERT: R 76 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6385 (mp) REVERT: R 216 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7904 (mtt180) outliers start: 32 outliers final: 23 residues processed: 97 average time/residue: 0.4151 time to fit residues: 42.9214 Evaluate side-chains 98 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 53 HIS Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 216 ARG Chi-restraints excluded: chain R residue 225 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.177024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159349 restraints weight = 7795.918| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.29 r_work: 0.3791 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6356 Z= 0.137 Angle : 0.518 7.448 8663 Z= 0.277 Chirality : 0.042 0.145 1040 Planarity : 0.003 0.036 1077 Dihedral : 6.967 53.866 929 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.89 % Allowed : 25.18 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.29), residues: 821 helix: 2.05 (0.29), residues: 315 sheet: -1.27 (0.34), residues: 204 loop : -1.54 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.018 0.001 TYR R 321 PHE 0.017 0.001 PHE R 288 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6353) covalent geometry : angle 0.51720 ( 8657) SS BOND : bond 0.00186 ( 3) SS BOND : angle 0.94339 ( 6) hydrogen bonds : bond 0.04211 ( 320) hydrogen bonds : angle 4.39636 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2143.99 seconds wall clock time: 37 minutes 14.71 seconds (2234.71 seconds total)