Starting phenix.real_space_refine on Tue Mar 3 16:22:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wvv_32859/03_2026/7wvv_32859.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wvv_32859/03_2026/7wvv_32859.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/7wvv_32859/03_2026/7wvv_32859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wvv_32859/03_2026/7wvv_32859.map" model { file = "/net/cci-nas-00/data/ceres_data/7wvv_32859/03_2026/7wvv_32859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wvv_32859/03_2026/7wvv_32859.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= 0.005 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 53 5.16 5 C 4528 2.51 5 N 1184 2.21 5 O 1255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 7020 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2319 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 284} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1778 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2510 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 367 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 1.50, per 1000 atoms: 0.21 Number of scatterers: 7020 At special positions: 0 Unit cell: (112.86, 119.13, 85.69, 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 53 16.00 O 1255 8.00 N 1184 7.00 C 4528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " 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: 0.53 Conformation dependent library (CDL) restraints added in 203.3 milliseconds 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 47.7% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 20 through 55 Proline residue: R 29 - end of helix removed outlier: 3.954A pdb=" N PHE R 53 " --> pdb=" O TRP R 49 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 77 removed outlier: 3.769A pdb=" N THR R 77 " --> pdb=" O SER R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 86 removed outlier: 3.699A pdb=" N LEU R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 Processing helix chain 'R' and resid 129 through 137 removed outlier: 3.649A pdb=" N ARG R 137 " --> pdb=" O ALA R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 163 Proline residue: R 149 - end of helix Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'R' and resid 186 through 210 Processing helix chain 'R' and resid 210 through 231 Processing helix chain 'R' and resid 237 through 267 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 274 Processing helix chain 'R' and resid 278 through 303 removed outlier: 3.741A pdb=" N ILE R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 316 Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.710A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 4.048A pdb=" N THR A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.981A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.609A pdb=" N LEU A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.629A pdb=" N VAL A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 26 removed outlier: 3.570A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.575A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'R' and resid 167 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192 removed outlier: 8.887A pdb=" N ALA A 221 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ALA A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.522A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.805A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.420A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.474A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.505A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.996A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.165A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1119 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: 1.05 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2230 1.34 - 1.46: 1716 1.46 - 1.58: 3146 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 7169 Sorted by residual: bond pdb=" SD FME L 1 " pdb=" CE FME L 1 " ideal model delta sigma weight residual 1.805 1.752 0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" CG FME L 1 " pdb=" SD FME L 1 " ideal model delta sigma weight residual 1.817 1.771 0.046 2.00e-02 2.50e+03 5.40e+00 bond pdb=" N FME L 1 " pdb=" CN FME L 1 " ideal model delta sigma weight residual 1.335 1.376 -0.041 2.00e-02 2.50e+03 4.27e+00 bond pdb=" N FME L 1 " pdb=" CA FME L 1 " ideal model delta sigma weight residual 1.458 1.436 0.022 1.90e-02 2.77e+03 1.36e+00 bond pdb=" CN FME L 1 " pdb=" O1 FME L 1 " ideal model delta sigma weight residual 1.221 1.241 -0.020 2.00e-02 2.50e+03 9.64e-01 ... (remaining 7164 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 9436 1.07 - 2.14: 223 2.14 - 3.22: 47 3.22 - 4.29: 11 4.29 - 5.36: 9 Bond angle restraints: 9726 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.72 110.98 2.74 1.30e+00 5.92e-01 4.44e+00 angle pdb=" CB MET R 197 " pdb=" CG MET R 197 " pdb=" SD MET R 197 " ideal model delta sigma weight residual 112.70 118.06 -5.36 3.00e+00 1.11e-01 3.19e+00 angle pdb=" NE ARG B 49 " pdb=" CZ ARG B 49 " pdb=" NH1 ARG B 49 " ideal model delta sigma weight residual 121.50 119.72 1.78 1.00e+00 1.00e+00 3.18e+00 angle pdb=" C ASP A 329 " pdb=" N THR A 330 " pdb=" CA THR A 330 " ideal model delta sigma weight residual 121.54 124.88 -3.34 1.91e+00 2.74e-01 3.05e+00 angle pdb=" N GLY R 232 " pdb=" CA GLY R 232 " pdb=" C GLY R 232 " ideal model delta sigma weight residual 113.18 117.16 -3.98 2.37e+00 1.78e-01 2.81e+00 ... (remaining 9721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3867 17.35 - 34.71: 300 34.71 - 52.06: 44 52.06 - 69.42: 5 69.42 - 86.77: 3 Dihedral angle restraints: 4219 sinusoidal: 1585 harmonic: 2634 Sorted by residual: dihedral pdb=" CA ASP B 254 " pdb=" CB ASP B 254 " pdb=" CG ASP B 254 " pdb=" OD1 ASP B 254 " ideal model delta sinusoidal sigma weight residual -30.00 -89.95 59.95 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CB GLU B 138 " pdb=" CG GLU B 138 " pdb=" CD GLU B 138 " pdb=" OE1 GLU B 138 " ideal model delta sinusoidal sigma weight residual 0.00 86.77 -86.77 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CG ARG B 48 " pdb=" CD ARG B 48 " pdb=" NE ARG B 48 " pdb=" CZ ARG B 48 " ideal model delta sinusoidal sigma weight residual -180.00 -137.11 -42.89 2 1.50e+01 4.44e-03 9.88e+00 ... (remaining 4216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 711 0.028 - 0.055: 261 0.055 - 0.083: 94 0.083 - 0.110: 59 0.110 - 0.138: 15 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1137 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 148 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO R 149 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 149 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 149 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO B 236 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 164 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C THR B 164 " 0.024 2.00e-02 2.50e+03 pdb=" O THR B 164 " -0.009 2.00e-02 2.50e+03 pdb=" N THR B 165 " -0.008 2.00e-02 2.50e+03 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1840 2.81 - 3.33: 6808 3.33 - 3.85: 11965 3.85 - 4.38: 13859 4.38 - 4.90: 24483 Nonbonded interactions: 58955 Sorted by model distance: nonbonded pdb=" OD1 ASN A 270 " pdb=" OG1 THR A 325 " model vdw 2.286 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.301 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.310 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.320 3.040 nonbonded pdb=" O PRO R 286 " pdb=" OG SER R 289 " model vdw 2.328 3.040 ... (remaining 58950 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: 0.970 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.120 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 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 : 0.002 0.053 7170 Z= 0.106 Angle : 0.446 5.362 9728 Z= 0.246 Chirality : 0.039 0.138 1140 Planarity : 0.003 0.038 1212 Dihedral : 12.210 86.772 2508 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.74 (0.28), residues: 898 helix: 1.85 (0.26), residues: 394 sheet: 0.37 (0.40), residues: 183 loop : -1.18 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.007 0.001 TYR A 231 PHE 0.019 0.001 PHE R 257 TRP 0.006 0.001 TRP B 169 HIS 0.003 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 7169) covalent geometry : angle 0.44631 ( 9726) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.94810 ( 2) hydrogen bonds : bond 0.19621 ( 386) hydrogen bonds : angle 7.05931 ( 1119) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.247 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.4510 time to fit residues: 60.3536 Evaluate side-chains 100 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.0020 chunk 74 optimal weight: 2.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN B 75 GLN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.167551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128896 restraints weight = 7176.617| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.83 r_work: 0.3377 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7170 Z= 0.198 Angle : 0.564 7.730 9728 Z= 0.302 Chirality : 0.042 0.138 1140 Planarity : 0.004 0.041 1212 Dihedral : 3.987 22.147 967 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.89 % Allowed : 12.67 % Favored : 85.44 % 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: 0.41 (0.27), residues: 898 helix: 1.46 (0.25), residues: 404 sheet: 0.14 (0.38), residues: 187 loop : -1.22 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 26 TYR 0.010 0.001 TYR B 59 PHE 0.015 0.002 PHE A 197 TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 7169) covalent geometry : angle 0.56315 ( 9726) SS BOND : bond 0.00085 ( 1) SS BOND : angle 1.80587 ( 2) hydrogen bonds : bond 0.04688 ( 386) hydrogen bonds : angle 5.25399 ( 1119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.223 Fit side-chains REVERT: R 147 VAL cc_start: 0.7823 (p) cc_final: 0.7436 (m) REVERT: R 214 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7960 (tpt) REVERT: A 233 LEU cc_start: 0.7617 (mp) cc_final: 0.7359 (mp) outliers start: 14 outliers final: 6 residues processed: 118 average time/residue: 0.4928 time to fit residues: 61.7221 Evaluate side-chains 113 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 64 optimal weight: 0.0060 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 72 optimal weight: 0.0570 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.171318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.134016 restraints weight = 7044.657| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.78 r_work: 0.3433 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7170 Z= 0.111 Angle : 0.484 7.594 9728 Z= 0.259 Chirality : 0.040 0.135 1140 Planarity : 0.004 0.040 1212 Dihedral : 3.811 23.235 967 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.75 % Allowed : 15.77 % Favored : 82.48 % 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: 0.53 (0.28), residues: 898 helix: 1.65 (0.25), residues: 410 sheet: 0.15 (0.37), residues: 186 loop : -1.32 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 26 TYR 0.008 0.001 TYR B 124 PHE 0.012 0.001 PHE B 199 TRP 0.018 0.001 TRP B 169 HIS 0.003 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 7169) covalent geometry : angle 0.48398 ( 9726) SS BOND : bond 0.00010 ( 1) SS BOND : angle 1.36930 ( 2) hydrogen bonds : bond 0.03977 ( 386) hydrogen bonds : angle 4.90895 ( 1119) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.257 Fit side-chains REVERT: R 147 VAL cc_start: 0.7694 (OUTLIER) cc_final: 0.7232 (m) REVERT: R 214 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7893 (tpt) REVERT: A 217 GLU cc_start: 0.7607 (tt0) cc_final: 0.7389 (tt0) outliers start: 13 outliers final: 5 residues processed: 116 average time/residue: 0.4625 time to fit residues: 57.1531 Evaluate side-chains 107 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN ** A 332 ASN ** 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 = 0.3921 r_free = 0.3921 target = 0.163442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124309 restraints weight = 7139.655| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.82 r_work: 0.3382 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7170 Z= 0.162 Angle : 0.520 8.435 9728 Z= 0.279 Chirality : 0.041 0.142 1140 Planarity : 0.004 0.041 1212 Dihedral : 4.039 24.107 967 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.10 % Allowed : 16.31 % Favored : 80.59 % 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: 0.38 (0.28), residues: 898 helix: 1.56 (0.25), residues: 409 sheet: -0.11 (0.37), residues: 192 loop : -1.33 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 219 TYR 0.009 0.001 TYR R 221 PHE 0.013 0.002 PHE A 197 TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7169) covalent geometry : angle 0.51962 ( 9726) SS BOND : bond 0.00187 ( 1) SS BOND : angle 1.89319 ( 2) hydrogen bonds : bond 0.04156 ( 386) hydrogen bonds : angle 5.00620 ( 1119) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.263 Fit side-chains REVERT: R 214 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7893 (tpt) REVERT: R 294 ASN cc_start: 0.8307 (t0) cc_final: 0.7931 (t0) REVERT: A 277 GLU cc_start: 0.7726 (pp20) cc_final: 0.7506 (pp20) outliers start: 23 outliers final: 9 residues processed: 117 average time/residue: 0.4815 time to fit residues: 59.9953 Evaluate side-chains 113 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 93 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 7 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN ** A 332 ASN ** 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 = 0.3931 r_free = 0.3931 target = 0.164542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125790 restraints weight = 7113.474| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.82 r_work: 0.3331 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7170 Z= 0.132 Angle : 0.499 8.679 9728 Z= 0.265 Chirality : 0.040 0.138 1140 Planarity : 0.004 0.041 1212 Dihedral : 4.028 25.868 967 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.83 % Allowed : 17.92 % Favored : 79.25 % 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: 0.39 (0.28), residues: 898 helix: 1.59 (0.25), residues: 409 sheet: -0.15 (0.36), residues: 192 loop : -1.32 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.007 0.001 TYR R 221 PHE 0.012 0.001 PHE B 199 TRP 0.017 0.001 TRP R 91 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7169) covalent geometry : angle 0.49869 ( 9726) SS BOND : bond 0.00175 ( 1) SS BOND : angle 1.76586 ( 2) hydrogen bonds : bond 0.03907 ( 386) hydrogen bonds : angle 4.88548 ( 1119) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.250 Fit side-chains REVERT: R 214 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7878 (tpt) REVERT: R 294 ASN cc_start: 0.8147 (t0) cc_final: 0.7776 (t0) REVERT: A 277 GLU cc_start: 0.7653 (pp20) cc_final: 0.7388 (pp20) REVERT: A 290 GLU cc_start: 0.7848 (pm20) cc_final: 0.7406 (pm20) outliers start: 21 outliers final: 10 residues processed: 123 average time/residue: 0.4803 time to fit residues: 62.6565 Evaluate side-chains 115 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 93 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.162188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122989 restraints weight = 7123.687| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.83 r_work: 0.3303 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7170 Z= 0.158 Angle : 0.526 9.367 9728 Z= 0.278 Chirality : 0.041 0.144 1140 Planarity : 0.004 0.042 1212 Dihedral : 4.130 26.711 967 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.50 % Allowed : 18.06 % Favored : 78.44 % 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: 0.33 (0.28), residues: 898 helix: 1.55 (0.25), residues: 409 sheet: -0.23 (0.36), residues: 194 loop : -1.32 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.008 0.001 TYR R 221 PHE 0.014 0.002 PHE B 199 TRP 0.016 0.001 TRP R 91 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7169) covalent geometry : angle 0.52560 ( 9726) SS BOND : bond 0.00293 ( 1) SS BOND : angle 2.01278 ( 2) hydrogen bonds : bond 0.04056 ( 386) hydrogen bonds : angle 4.96003 ( 1119) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.215 Fit side-chains REVERT: R 214 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7854 (tpt) REVERT: R 294 ASN cc_start: 0.8288 (t0) cc_final: 0.7772 (t0) REVERT: A 17 LYS cc_start: 0.7171 (mppt) cc_final: 0.6956 (mptp) REVERT: A 277 GLU cc_start: 0.7656 (pp20) cc_final: 0.7378 (pp20) REVERT: A 290 GLU cc_start: 0.7875 (pm20) cc_final: 0.7439 (pm20) outliers start: 26 outliers final: 15 residues processed: 122 average time/residue: 0.4677 time to fit residues: 60.4873 Evaluate side-chains 121 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.162333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123376 restraints weight = 7136.071| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.81 r_work: 0.3303 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7170 Z= 0.146 Angle : 0.522 9.871 9728 Z= 0.274 Chirality : 0.041 0.139 1140 Planarity : 0.004 0.042 1212 Dihedral : 4.138 27.872 967 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.83 % Allowed : 19.27 % Favored : 77.90 % 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: 0.37 (0.28), residues: 898 helix: 1.59 (0.25), residues: 409 sheet: -0.22 (0.36), residues: 194 loop : -1.32 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.007 0.001 TYR R 221 PHE 0.013 0.001 PHE B 199 TRP 0.016 0.001 TRP R 91 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 7169) covalent geometry : angle 0.52100 ( 9726) SS BOND : bond 0.00298 ( 1) SS BOND : angle 1.94695 ( 2) hydrogen bonds : bond 0.03945 ( 386) hydrogen bonds : angle 4.91737 ( 1119) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.185 Fit side-chains REVERT: R 214 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7800 (tpt) REVERT: R 294 ASN cc_start: 0.8309 (t0) cc_final: 0.7922 (t0) REVERT: A 17 LYS cc_start: 0.7151 (mppt) cc_final: 0.6942 (mptp) REVERT: A 277 GLU cc_start: 0.7652 (pp20) cc_final: 0.7351 (pp20) REVERT: A 290 GLU cc_start: 0.7964 (pm20) cc_final: 0.7483 (pm20) REVERT: B 49 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7385 (mtp85) outliers start: 21 outliers final: 13 residues processed: 119 average time/residue: 0.5123 time to fit residues: 64.4337 Evaluate side-chains 118 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.162636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124105 restraints weight = 7126.638| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.80 r_work: 0.3310 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7170 Z= 0.140 Angle : 0.522 10.337 9728 Z= 0.276 Chirality : 0.041 0.144 1140 Planarity : 0.004 0.042 1212 Dihedral : 4.106 28.095 967 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.37 % Allowed : 19.81 % Favored : 76.82 % 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: 0.35 (0.28), residues: 898 helix: 1.61 (0.25), residues: 410 sheet: -0.23 (0.36), residues: 194 loop : -1.40 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.010 0.001 TYR B 124 PHE 0.014 0.001 PHE B 199 TRP 0.016 0.001 TRP R 91 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7169) covalent geometry : angle 0.52161 ( 9726) SS BOND : bond 0.00299 ( 1) SS BOND : angle 1.93454 ( 2) hydrogen bonds : bond 0.03884 ( 386) hydrogen bonds : angle 4.86810 ( 1119) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.262 Fit side-chains REVERT: R 214 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7841 (tpt) REVERT: R 294 ASN cc_start: 0.8343 (t0) cc_final: 0.7849 (t0) REVERT: A 17 LYS cc_start: 0.7133 (mppt) cc_final: 0.6930 (mptp) REVERT: A 21 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7349 (tmmm) REVERT: A 277 GLU cc_start: 0.7666 (pp20) cc_final: 0.7369 (pp20) REVERT: A 290 GLU cc_start: 0.7958 (pm20) cc_final: 0.7452 (pm20) REVERT: B 78 LYS cc_start: 0.8614 (mptm) cc_final: 0.8403 (mptt) REVERT: B 219 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7584 (tpp-160) outliers start: 25 outliers final: 14 residues processed: 124 average time/residue: 0.4921 time to fit residues: 64.5710 Evaluate side-chains 118 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.163215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124672 restraints weight = 7139.996| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.81 r_work: 0.3318 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7170 Z= 0.134 Angle : 0.526 11.062 9728 Z= 0.278 Chirality : 0.041 0.143 1140 Planarity : 0.004 0.042 1212 Dihedral : 4.110 27.990 967 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.56 % Allowed : 20.35 % Favored : 77.09 % 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: 0.39 (0.28), residues: 898 helix: 1.66 (0.25), residues: 410 sheet: -0.19 (0.36), residues: 194 loop : -1.41 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.017 0.001 TYR B 59 PHE 0.013 0.001 PHE B 199 TRP 0.016 0.001 TRP R 91 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 7169) covalent geometry : angle 0.52518 ( 9726) SS BOND : bond 0.00231 ( 1) SS BOND : angle 1.87262 ( 2) hydrogen bonds : bond 0.03830 ( 386) hydrogen bonds : angle 4.80257 ( 1119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.290 Fit side-chains REVERT: R 147 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7333 (m) REVERT: R 214 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7769 (tpt) REVERT: R 294 ASN cc_start: 0.8332 (t0) cc_final: 0.7837 (t0) REVERT: A 17 LYS cc_start: 0.7145 (mppt) cc_final: 0.6944 (mptp) REVERT: A 21 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7332 (tmmm) REVERT: A 277 GLU cc_start: 0.7660 (pp20) cc_final: 0.7366 (pp20) REVERT: A 290 GLU cc_start: 0.7939 (pm20) cc_final: 0.7436 (pm20) REVERT: B 219 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7578 (tpp-160) REVERT: B 234 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.7824 (m-80) outliers start: 19 outliers final: 12 residues processed: 117 average time/residue: 0.4736 time to fit residues: 58.9900 Evaluate side-chains 118 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 65 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125877 restraints weight = 7134.769| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.81 r_work: 0.3337 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7170 Z= 0.126 Angle : 0.522 10.836 9728 Z= 0.276 Chirality : 0.040 0.141 1140 Planarity : 0.004 0.042 1212 Dihedral : 4.078 27.727 967 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.29 % Allowed : 21.29 % Favored : 76.42 % 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: 0.42 (0.28), residues: 898 helix: 1.68 (0.26), residues: 413 sheet: -0.17 (0.36), residues: 194 loop : -1.43 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.018 0.001 TYR B 59 PHE 0.013 0.001 PHE B 199 TRP 0.016 0.001 TRP R 91 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7169) covalent geometry : angle 0.52101 ( 9726) SS BOND : bond 0.00142 ( 1) SS BOND : angle 1.82531 ( 2) hydrogen bonds : bond 0.03722 ( 386) hydrogen bonds : angle 4.73486 ( 1119) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.265 Fit side-chains REVERT: R 147 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7272 (m) REVERT: R 214 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7686 (tpt) REVERT: R 294 ASN cc_start: 0.8312 (t0) cc_final: 0.7823 (t0) REVERT: A 21 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7327 (tmmm) REVERT: A 277 GLU cc_start: 0.7661 (pp20) cc_final: 0.7368 (pp20) REVERT: A 290 GLU cc_start: 0.7922 (pm20) cc_final: 0.7419 (pm20) REVERT: B 96 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7500 (ptp-170) REVERT: B 234 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8014 (m-80) outliers start: 17 outliers final: 12 residues processed: 118 average time/residue: 0.5068 time to fit residues: 63.4652 Evaluate side-chains 120 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 88 optimal weight: 0.0370 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 0.0870 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.173162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137694 restraints weight = 6892.746| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.62 r_work: 0.3401 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7170 Z= 0.116 Angle : 0.516 10.662 9728 Z= 0.272 Chirality : 0.040 0.139 1140 Planarity : 0.004 0.042 1212 Dihedral : 4.039 27.324 967 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.29 % Allowed : 21.16 % Favored : 76.55 % 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: 0.47 (0.28), residues: 898 helix: 1.73 (0.26), residues: 413 sheet: -0.16 (0.36), residues: 194 loop : -1.42 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 205 TYR 0.012 0.001 TYR B 124 PHE 0.012 0.001 PHE B 199 TRP 0.015 0.001 TRP R 91 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7169) covalent geometry : angle 0.51533 ( 9726) SS BOND : bond 0.00092 ( 1) SS BOND : angle 1.68901 ( 2) hydrogen bonds : bond 0.03628 ( 386) hydrogen bonds : angle 4.67340 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2797.43 seconds wall clock time: 48 minutes 19.19 seconds (2899.19 seconds total)