Starting phenix.real_space_refine on Wed Mar 12 01:52:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wvv_32859/03_2025/7wvv_32859.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wvv_32859/03_2025/7wvv_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_2025/7wvv_32859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wvv_32859/03_2025/7wvv_32859.map" model { file = "/net/cci-nas-00/data/ceres_data/7wvv_32859/03_2025/7wvv_32859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wvv_32859/03_2025/7wvv_32859.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'ARG:plan': 1, 'ASP: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: {'GLU:plan': 2, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 4.98, per 1000 atoms: 0.71 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: 1.64 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.72 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: 1.97 Time building geometry restraints manager: 1.97 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: 1.170 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.460 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 38.220 ------------------------------------------------------------------------------- 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 7169 Z= 0.125 Angle : 0.446 5.362 9726 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 : 7.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (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 TRP 0.006 0.001 TRP B 169 HIS 0.003 0.000 HIS B 91 PHE 0.019 0.001 PHE R 257 TYR 0.007 0.001 TYR A 231 ARG 0.006 0.000 ARG B 49 *********************** 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 : 0.801 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.9714 time to fit residues: 130.7693 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 : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 0.0970 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 347 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.175493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138635 restraints weight = 7038.304| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.78 r_work: 0.3494 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7169 Z= 0.177 Angle : 0.508 7.154 9726 Z= 0.271 Chirality : 0.041 0.131 1140 Planarity : 0.004 0.041 1212 Dihedral : 3.707 22.177 967 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.62 % Allowed : 11.99 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.28), residues: 898 helix: 1.65 (0.25), residues: 405 sheet: 0.23 (0.38), residues: 183 loop : -1.30 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE R 163 TYR 0.007 0.001 TYR B 289 ARG 0.006 0.000 ARG R 26 *********************** 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 129 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.770 Fit side-chains REVERT: R 214 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7798 (tpt) outliers start: 12 outliers final: 4 residues processed: 121 average time/residue: 1.0303 time to fit residues: 133.3816 Evaluate side-chains 111 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 83 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.0170 overall best weight: 0.5220 ------------------------------------------------------------------------------- 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 C 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.175001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139114 restraints weight = 7045.164| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.69 r_work: 0.3455 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7169 Z= 0.172 Angle : 0.485 6.853 9726 Z= 0.260 Chirality : 0.040 0.134 1140 Planarity : 0.004 0.041 1212 Dihedral : 3.756 22.428 967 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.56 % Allowed : 14.56 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.28), residues: 898 helix: 1.71 (0.25), residues: 410 sheet: 0.20 (0.38), residues: 186 loop : -1.28 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE A 197 TYR 0.010 0.001 TYR B 124 ARG 0.005 0.000 ARG R 26 *********************** 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 134 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.833 Fit side-chains REVERT: R 147 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7296 (m) REVERT: R 214 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7831 (tpt) outliers start: 19 outliers final: 7 residues processed: 125 average time/residue: 0.9343 time to fit residues: 125.1125 Evaluate side-chains 117 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 264 SER Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 93 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 81 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.165537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128449 restraints weight = 7125.026| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.72 r_work: 0.3371 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7169 Z= 0.215 Angle : 0.513 8.357 9726 Z= 0.273 Chirality : 0.041 0.141 1140 Planarity : 0.004 0.041 1212 Dihedral : 3.959 23.258 967 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.23 % Allowed : 16.04 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.28), residues: 898 helix: 1.66 (0.25), residues: 409 sheet: -0.00 (0.37), residues: 188 loop : -1.34 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS C 44 PHE 0.013 0.002 PHE A 197 TYR 0.009 0.001 TYR B 124 ARG 0.006 0.000 ARG B 219 *********************** 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 133 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.720 Fit side-chains REVERT: R 147 VAL cc_start: 0.7694 (OUTLIER) cc_final: 0.7315 (m) REVERT: R 214 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7823 (tpt) REVERT: R 294 ASN cc_start: 0.8223 (t0) cc_final: 0.7847 (t0) outliers start: 24 outliers final: 11 residues processed: 122 average time/residue: 0.9854 time to fit residues: 128.1883 Evaluate side-chains 120 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 32 ARG Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 264 SER 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 C residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.163103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124119 restraints weight = 7019.952| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.80 r_work: 0.3446 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7169 Z= 0.246 Angle : 0.529 8.880 9726 Z= 0.278 Chirality : 0.041 0.138 1140 Planarity : 0.004 0.041 1212 Dihedral : 4.081 25.331 967 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.96 % Allowed : 18.46 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.28), residues: 898 helix: 1.55 (0.25), residues: 410 sheet: -0.20 (0.36), residues: 192 loop : -1.30 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 91 HIS 0.002 0.001 HIS C 44 PHE 0.011 0.002 PHE A 197 TYR 0.009 0.001 TYR R 221 ARG 0.007 0.001 ARG B 219 *********************** 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 129 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.780 Fit side-chains REVERT: R 147 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7386 (m) REVERT: R 214 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7893 (tpt) REVERT: R 294 ASN cc_start: 0.8299 (t0) cc_final: 0.7907 (t0) REVERT: B 188 MET cc_start: 0.8167 (mmm) cc_final: 0.7919 (mmm) outliers start: 22 outliers final: 13 residues processed: 118 average time/residue: 0.9835 time to fit residues: 123.9386 Evaluate side-chains 115 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 196 THR Chi-restraints excluded: chain R residue 214 MET Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 264 SER 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 C residue 38 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 45 optimal weight: 0.0570 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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 B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.166876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128039 restraints weight = 7078.221| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.84 r_work: 0.3366 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7169 Z= 0.159 Angle : 0.491 9.372 9726 Z= 0.257 Chirality : 0.040 0.143 1140 Planarity : 0.004 0.040 1212 Dihedral : 3.949 26.983 967 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.23 % Allowed : 19.00 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 898 helix: 1.65 (0.26), residues: 411 sheet: -0.17 (0.36), residues: 192 loop : -1.26 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 91 HIS 0.002 0.000 HIS B 54 PHE 0.009 0.001 PHE A 197 TYR 0.006 0.001 TYR R 221 ARG 0.006 0.000 ARG B 219 *********************** 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 130 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.853 Fit side-chains REVERT: R 147 VAL cc_start: 0.7690 (p) cc_final: 0.7287 (m) REVERT: R 214 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7734 (tpt) REVERT: R 294 ASN cc_start: 0.8208 (t0) cc_final: 0.7877 (t0) REVERT: A 17 LYS cc_start: 0.7170 (tppt) cc_final: 0.6961 (mptp) outliers start: 24 outliers final: 10 residues processed: 116 average time/residue: 0.9961 time to fit residues: 123.3666 Evaluate side-chains 112 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 LEU 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 214 MET Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 93 ILE 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 77 optimal weight: 3.9990 chunk 40 optimal weight: 0.0070 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.160597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121267 restraints weight = 7107.362| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.82 r_work: 0.3272 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7169 Z= 0.279 Angle : 0.547 10.001 9726 Z= 0.289 Chirality : 0.042 0.140 1140 Planarity : 0.004 0.042 1212 Dihedral : 4.211 26.419 967 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.96 % Allowed : 19.54 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.28), residues: 898 helix: 1.54 (0.25), residues: 409 sheet: -0.18 (0.38), residues: 180 loop : -1.38 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 189 PHE 0.014 0.002 PHE A 197 TYR 0.010 0.001 TYR B 124 ARG 0.006 0.001 ARG B 219 *********************** 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 122 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.735 Fit side-chains REVERT: R 147 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7490 (m) REVERT: R 214 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7895 (tpt) REVERT: R 294 ASN cc_start: 0.8336 (t0) cc_final: 0.7815 (t0) REVERT: A 241 MET cc_start: 0.7389 (tpt) cc_final: 0.6639 (tpt) REVERT: B 219 ARG cc_start: 0.7855 (tpp80) cc_final: 0.7507 (tpp-160) outliers start: 22 outliers final: 12 residues processed: 113 average time/residue: 0.9533 time to fit residues: 115.1410 Evaluate side-chains 114 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 214 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 264 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 34 optimal weight: 0.1980 chunk 88 optimal weight: 0.0050 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.164448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127864 restraints weight = 7050.213| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.68 r_work: 0.3367 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7169 Z= 0.168 Angle : 0.500 10.168 9726 Z= 0.261 Chirality : 0.040 0.141 1140 Planarity : 0.004 0.041 1212 Dihedral : 4.068 28.287 967 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.10 % Allowed : 19.41 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 898 helix: 1.67 (0.26), residues: 411 sheet: -0.23 (0.36), residues: 194 loop : -1.31 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 91 HIS 0.002 0.000 HIS B 54 PHE 0.010 0.001 PHE A 197 TYR 0.010 0.001 TYR B 124 ARG 0.007 0.000 ARG R 26 *********************** 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 125 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.750 Fit side-chains REVERT: R 147 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7372 (m) REVERT: R 214 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7607 (tpt) REVERT: R 294 ASN cc_start: 0.8301 (t0) cc_final: 0.7942 (t0) REVERT: A 241 MET cc_start: 0.7507 (tpt) cc_final: 0.6920 (tpt) outliers start: 23 outliers final: 10 residues processed: 116 average time/residue: 0.9601 time to fit residues: 119.4371 Evaluate side-chains 108 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 214 MET Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 264 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 56 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.164920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124853 restraints weight = 7172.397| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.94 r_work: 0.3438 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7169 Z= 0.186 Angle : 0.510 10.964 9726 Z= 0.268 Chirality : 0.040 0.139 1140 Planarity : 0.004 0.042 1212 Dihedral : 4.043 27.464 967 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.56 % Allowed : 19.95 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.28), residues: 898 helix: 1.71 (0.26), residues: 411 sheet: -0.16 (0.37), residues: 185 loop : -1.36 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 91 HIS 0.002 0.000 HIS A 189 PHE 0.009 0.001 PHE R 210 TYR 0.016 0.001 TYR B 59 ARG 0.007 0.000 ARG B 219 *********************** 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 116 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.897 Fit side-chains REVERT: R 147 VAL cc_start: 0.7684 (OUTLIER) cc_final: 0.7276 (m) REVERT: R 214 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7611 (tpt) REVERT: R 294 ASN cc_start: 0.8301 (t0) cc_final: 0.7949 (t0) REVERT: A 17 LYS cc_start: 0.7096 (tppt) cc_final: 0.6885 (mptp) REVERT: B 219 ARG cc_start: 0.7933 (tpp80) cc_final: 0.7710 (tpp-160) REVERT: B 234 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.7478 (m-80) outliers start: 19 outliers final: 12 residues processed: 108 average time/residue: 1.0203 time to fit residues: 117.6143 Evaluate side-chains 110 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 264 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.0060 chunk 43 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 0.0980 chunk 88 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.176078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138925 restraints weight = 6974.034| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.73 r_work: 0.3400 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7169 Z= 0.154 Angle : 0.493 10.764 9726 Z= 0.260 Chirality : 0.040 0.137 1140 Planarity : 0.004 0.041 1212 Dihedral : 3.971 27.007 967 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.29 % Allowed : 20.75 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 898 helix: 1.76 (0.26), residues: 412 sheet: -0.07 (0.37), residues: 190 loop : -1.31 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 91 HIS 0.002 0.000 HIS B 54 PHE 0.009 0.001 PHE R 118 TYR 0.013 0.001 TYR B 124 ARG 0.007 0.000 ARG B 219 ********************** 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 123 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.702 Fit side-chains REVERT: R 147 VAL cc_start: 0.7605 (OUTLIER) cc_final: 0.7210 (m) REVERT: R 214 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7610 (tpt) REVERT: R 294 ASN cc_start: 0.8202 (t0) cc_final: 0.7731 (t0) REVERT: A 20 ASP cc_start: 0.7676 (m-30) cc_final: 0.7445 (m-30) REVERT: A 201 ASP cc_start: 0.7785 (m-30) cc_final: 0.7360 (t0) REVERT: A 277 GLU cc_start: 0.7730 (pp20) cc_final: 0.7493 (pp20) REVERT: B 234 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.7543 (m-80) outliers start: 17 outliers final: 7 residues processed: 117 average time/residue: 1.0141 time to fit residues: 126.4971 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 : 0.764 ------------------------------------------------------------------------------- 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 188 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 24 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.160487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121461 restraints weight = 7143.099| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.82 r_work: 0.3278 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7169 Z= 0.284 Angle : 0.565 11.405 9726 Z= 0.298 Chirality : 0.042 0.138 1140 Planarity : 0.004 0.043 1212 Dihedral : 4.278 26.534 967 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.48 % Allowed : 22.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.28), residues: 898 helix: 1.60 (0.25), residues: 410 sheet: -0.17 (0.38), residues: 180 loop : -1.49 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 91 HIS 0.003 0.001 HIS C 44 PHE 0.014 0.002 PHE R 210 TYR 0.010 0.002 TYR R 221 ARG 0.005 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5702.32 seconds wall clock time: 97 minutes 52.81 seconds (5872.81 seconds total)