Starting phenix.real_space_refine on Thu Mar 13 00:08:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oya_20223/03_2025/6oya_20223.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oya_20223/03_2025/6oya_20223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oya_20223/03_2025/6oya_20223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oya_20223/03_2025/6oya_20223.map" model { file = "/net/cci-nas-00/data/ceres_data/6oya_20223/03_2025/6oya_20223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oya_20223/03_2025/6oya_20223.cif" } resolution = 3.3 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= -0.023 sd= 0.464 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 67 5.16 5 C 5312 2.51 5 N 1389 2.21 5 O 1553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8321 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1655 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 495 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2592 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 18, 'TRANS': 307} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.95, per 1000 atoms: 0.72 Number of scatterers: 8321 At special positions: 0 Unit cell: (85.86, 117.66, 113.42, 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 67 16.00 O 1553 8.00 N 1389 7.00 C 5312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 953.2 milliseconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 36.6% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 6 through 27 removed outlier: 3.752A pdb=" N GLU A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.609A pdb=" N ILE A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.521A pdb=" N CYS A 210 " --> pdb=" O TRP A 207 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 211 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 250 removed outlier: 3.566A pdb=" N MET A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 274 removed outlier: 4.122A pdb=" N GLU A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 Processing helix chain 'A' and resid 326 through 348 removed outlier: 3.670A pdb=" N ASP A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.863A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.767A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 25 Processing helix chain 'G' and resid 32 through 47 removed outlier: 3.672A pdb=" N ARG G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 51 removed outlier: 3.897A pdb=" N ASP G 51 " --> pdb=" O SER G 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 48 through 51' Processing helix chain 'R' and resid 14 through 18 removed outlier: 4.172A pdb=" N THR R 17 " --> pdb=" O SER R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 31 removed outlier: 4.548A pdb=" N TYR R 30 " --> pdb=" O PRO R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 65 Proline residue: R 53 - end of helix removed outlier: 4.382A pdb=" N THR R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU R 59 " --> pdb=" O ASN R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 89 Processing helix chain 'R' and resid 89 through 101 removed outlier: 4.260A pdb=" N THR R 93 " --> pdb=" O GLY R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 140 Processing helix chain 'R' and resid 149 through 169 removed outlier: 3.704A pdb=" N ALA R 153 " --> pdb=" O GLY R 149 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE R 154 " --> pdb=" O GLU R 150 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET R 155 " --> pdb=" O ASN R 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 211 Processing helix chain 'R' and resid 212 through 235 removed outlier: 3.673A pdb=" N ALA R 233 " --> pdb=" O THR R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 263 removed outlier: 3.856A pdb=" N LYS R 248 " --> pdb=" O GLN R 244 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 278 removed outlier: 3.966A pdb=" N ALA R 269 " --> pdb=" O TRP R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 307 removed outlier: 3.904A pdb=" N ILE R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Proline residue: R 291 - end of helix removed outlier: 3.615A pdb=" N SER R 298 " --> pdb=" O PHE R 294 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA R 299 " --> pdb=" O ALA R 295 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL R 300 " --> pdb=" O LYS R 296 " (cutoff:3.500A) Proline residue: R 303 - end of helix Processing helix chain 'R' and resid 312 through 322 removed outlier: 3.856A pdb=" N CYS R 316 " --> pdb=" O GLN R 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 removed outlier: 7.047A pdb=" N VAL A 30 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N PHE A 195 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 183 " --> pdb=" O MET A 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.712A pdb=" N LEU A 33 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 217 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.953A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 61 removed outlier: 7.262A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N MET B 61 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.698A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.086A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 233 through 234 removed outlier: 6.899A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.576A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.623A pdb=" N VAL N 12 " --> pdb=" O THR N 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'N' and resid 45 through 51 removed outlier: 6.340A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 4 through 5 327 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2672 1.35 - 1.47: 2121 1.47 - 1.59: 3609 1.59 - 1.71: 0 1.71 - 1.84: 99 Bond restraints: 8501 Sorted by residual: bond pdb=" CB ASP A 189 " pdb=" CG ASP A 189 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.25e+00 bond pdb=" C ILE R 214 " pdb=" N PRO R 215 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.20e+00 bond pdb=" C ILE R 290 " pdb=" N PRO R 291 " ideal model delta sigma weight residual 1.336 1.353 -0.018 1.23e-02 6.61e+03 2.12e+00 bond pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " ideal model delta sigma weight residual 1.532 1.554 -0.022 1.56e-02 4.11e+03 2.00e+00 bond pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 1.460 1.479 -0.020 1.42e-02 4.96e+03 1.91e+00 ... (remaining 8496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 11183 2.19 - 4.38: 261 4.38 - 6.57: 35 6.57 - 8.76: 18 8.76 - 10.96: 5 Bond angle restraints: 11502 Sorted by residual: angle pdb=" C ASN R 310 " pdb=" N LYS R 311 " pdb=" CA LYS R 311 " ideal model delta sigma weight residual 121.54 129.49 -7.95 1.91e+00 2.74e-01 1.73e+01 angle pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " pdb=" CG ASP A 189 " ideal model delta sigma weight residual 112.60 116.47 -3.87 1.00e+00 1.00e+00 1.50e+01 angle pdb=" N PRO R 170 " pdb=" CA PRO R 170 " pdb=" C PRO R 170 " ideal model delta sigma weight residual 110.70 115.28 -4.58 1.22e+00 6.72e-01 1.41e+01 angle pdb=" N ALA R 169 " pdb=" CA ALA R 169 " pdb=" C ALA R 169 " ideal model delta sigma weight residual 109.81 118.10 -8.29 2.21e+00 2.05e-01 1.41e+01 angle pdb=" C LEU B 126 " pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 122.82 127.91 -5.09 1.42e+00 4.96e-01 1.28e+01 ... (remaining 11497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4436 17.68 - 35.36: 499 35.36 - 53.04: 74 53.04 - 70.72: 21 70.72 - 88.40: 9 Dihedral angle restraints: 5039 sinusoidal: 1986 harmonic: 3053 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 163.25 -70.25 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual -86.00 -132.79 46.79 1 1.00e+01 1.00e-02 3.03e+01 dihedral pdb=" CA CYS B 166 " pdb=" C CYS B 166 " pdb=" N ALA B 167 " pdb=" CA ALA B 167 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 5036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 957 0.054 - 0.108: 247 0.108 - 0.161: 59 0.161 - 0.215: 10 0.215 - 0.269: 3 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CB THR N 28 " pdb=" CA THR N 28 " pdb=" OG1 THR N 28 " pdb=" CG2 THR N 28 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ASP A 189 " pdb=" N ASP A 189 " pdb=" C ASP A 189 " pdb=" CB ASP A 189 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE B 80 " pdb=" CA ILE B 80 " pdb=" CG1 ILE B 80 " pdb=" CG2 ILE B 80 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1273 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 170 " 0.062 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO R 171 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO R 171 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 171 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 70 " 0.044 5.00e-02 4.00e+02 6.71e-02 7.19e+00 pdb=" N PRO R 71 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO R 71 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 71 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 283 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.58e+00 pdb=" N PRO A 284 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.033 5.00e-02 4.00e+02 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2821 2.84 - 3.36: 7395 3.36 - 3.87: 13818 3.87 - 4.39: 15242 4.39 - 4.90: 26585 Nonbonded interactions: 65861 Sorted by model distance: nonbonded pdb=" OG1 THR A 320 " pdb=" OD2 ASP A 324 " model vdw 2.329 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.331 3.040 nonbonded pdb=" OE1 GLU B 226 " pdb=" OH TYR N 32 " model vdw 2.341 3.040 nonbonded pdb=" O SER B 84 " pdb=" OG SER B 84 " model vdw 2.347 3.040 nonbonded pdb=" NZ LYS A 341 " pdb=" OG1 THR R 243 " model vdw 2.351 3.120 ... (remaining 65856 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: 1.080 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.100 Find NCS groups from input model: 0.100 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8501 Z= 0.258 Angle : 0.877 10.956 11502 Z= 0.470 Chirality : 0.054 0.269 1276 Planarity : 0.007 0.094 1468 Dihedral : 15.281 88.402 3066 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.11 % Allowed : 10.19 % Favored : 89.70 % 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: -4.69 (0.20), residues: 1042 helix: -2.67 (0.19), residues: 369 sheet: -2.86 (0.31), residues: 206 loop : -3.55 (0.22), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.024 0.002 PHE B 151 TYR 0.025 0.002 TYR R 301 ARG 0.004 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8849 (tt0) cc_final: 0.8580 (tt0) REVERT: A 212 GLU cc_start: 0.8663 (tt0) cc_final: 0.8406 (tm-30) REVERT: A 240 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8953 (tp-100) REVERT: A 267 LYS cc_start: 0.7444 (mmpt) cc_final: 0.7015 (ttpt) REVERT: A 302 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8825 (mm110) REVERT: A 326 GLN cc_start: 0.8268 (mm110) cc_final: 0.7871 (mm110) REVERT: A 337 ASP cc_start: 0.8694 (t0) cc_final: 0.8387 (t0) REVERT: B 125 ASN cc_start: 0.8847 (t0) cc_final: 0.8483 (t0) REVERT: B 264 TYR cc_start: 0.8696 (m-80) cc_final: 0.8465 (m-10) REVERT: B 289 TYR cc_start: 0.8239 (m-10) cc_final: 0.7900 (m-10) REVERT: B 308 LEU cc_start: 0.9212 (mm) cc_final: 0.8645 (mt) REVERT: B 333 ASP cc_start: 0.7945 (p0) cc_final: 0.7723 (p0) REVERT: B 337 LYS cc_start: 0.8604 (mttt) cc_final: 0.8246 (mmtm) REVERT: B 339 TRP cc_start: 0.8548 (m100) cc_final: 0.8082 (m100) REVERT: G 51 ASP cc_start: 0.7973 (t0) cc_final: 0.7268 (t70) REVERT: G 65 LYS cc_start: 0.8080 (mttt) cc_final: 0.7872 (mttm) REVERT: N 6 GLU cc_start: 0.7804 (mp0) cc_final: 0.7425 (mp0) REVERT: N 22 CYS cc_start: 0.7485 (t) cc_final: 0.7184 (t) REVERT: N 76 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8253 (mptt) REVERT: N 77 ASN cc_start: 0.7865 (t0) cc_final: 0.7376 (t0) REVERT: N 112 SER cc_start: 0.8901 (m) cc_final: 0.8679 (m) REVERT: N 123 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8281 (tp40) REVERT: R 44 MET cc_start: 0.8555 (mmp) cc_final: 0.7571 (mmm) REVERT: R 60 TYR cc_start: 0.8569 (t80) cc_final: 0.8301 (t80) REVERT: R 78 ASN cc_start: 0.9040 (t0) cc_final: 0.8721 (t0) REVERT: R 134 GLU cc_start: 0.8259 (pt0) cc_final: 0.7944 (pt0) REVERT: R 147 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: R 155 MET cc_start: 0.8488 (ttt) cc_final: 0.8274 (ttm) REVERT: R 183 MET cc_start: 0.8629 (mmm) cc_final: 0.8298 (mmt) REVERT: R 236 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8092 (mm110) REVERT: R 308 MET cc_start: 0.8655 (mmm) cc_final: 0.8046 (mmm) REVERT: R 310 ASN cc_start: 0.8921 (t0) cc_final: 0.8233 (t0) REVERT: R 317 MET cc_start: 0.8656 (mtp) cc_final: 0.8413 (mtp) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.2078 time to fit residues: 74.9824 Evaluate side-chains 205 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS B 6 GLN B 13 GLN B 62 HIS B 91 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN R 73 ASN R 310 ASN R 312 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.111774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.095237 restraints weight = 16532.776| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.54 r_work: 0.3207 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8501 Z= 0.198 Angle : 0.625 8.557 11502 Z= 0.325 Chirality : 0.042 0.180 1276 Planarity : 0.004 0.050 1468 Dihedral : 5.769 69.617 1145 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.77 % Allowed : 16.83 % Favored : 81.40 % 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: -3.08 (0.23), residues: 1042 helix: -0.71 (0.26), residues: 360 sheet: -2.27 (0.34), residues: 200 loop : -3.01 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 318 PHE 0.013 0.001 PHE B 151 TYR 0.019 0.002 TYR R 301 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9089 (tt0) cc_final: 0.8822 (tt0) REVERT: A 182 GLU cc_start: 0.8466 (tt0) cc_final: 0.8236 (tp30) REVERT: A 194 MET cc_start: 0.8871 (mtt) cc_final: 0.8182 (mtp) REVERT: A 212 GLU cc_start: 0.9031 (tt0) cc_final: 0.8793 (tm-30) REVERT: A 240 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8315 (tp40) REVERT: A 268 ASP cc_start: 0.7000 (m-30) cc_final: 0.6357 (p0) REVERT: A 302 GLN cc_start: 0.9385 (mm-40) cc_final: 0.8907 (mm110) REVERT: A 326 GLN cc_start: 0.8682 (mm110) cc_final: 0.8273 (mm110) REVERT: A 337 ASP cc_start: 0.9341 (t0) cc_final: 0.8965 (t0) REVERT: B 17 GLN cc_start: 0.7813 (mt0) cc_final: 0.7554 (tm-30) REVERT: B 19 ARG cc_start: 0.7826 (tmt-80) cc_final: 0.6996 (ttm-80) REVERT: B 101 MET cc_start: 0.9032 (mmm) cc_final: 0.8767 (mmm) REVERT: B 125 ASN cc_start: 0.8941 (t0) cc_final: 0.8497 (t0) REVERT: B 186 ASP cc_start: 0.8299 (p0) cc_final: 0.7922 (p0) REVERT: B 228 ASP cc_start: 0.8825 (m-30) cc_final: 0.8096 (m-30) REVERT: B 235 PHE cc_start: 0.8987 (t80) cc_final: 0.8628 (t80) REVERT: B 262 MET cc_start: 0.8611 (mmm) cc_final: 0.8367 (mmt) REVERT: B 293 ASN cc_start: 0.7761 (t0) cc_final: 0.7356 (t0) REVERT: B 308 LEU cc_start: 0.9322 (mm) cc_final: 0.8960 (mp) REVERT: B 337 LYS cc_start: 0.8323 (mttt) cc_final: 0.8099 (mmtm) REVERT: B 339 TRP cc_start: 0.8875 (m100) cc_final: 0.8417 (m100) REVERT: G 65 LYS cc_start: 0.7868 (mttt) cc_final: 0.7634 (mttm) REVERT: N 22 CYS cc_start: 0.7783 (t) cc_final: 0.7471 (t) REVERT: N 76 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8239 (mptt) REVERT: N 77 ASN cc_start: 0.8243 (t0) cc_final: 0.7706 (t0) REVERT: N 123 GLN cc_start: 0.8981 (tp-100) cc_final: 0.8419 (tp-100) REVERT: R 60 TYR cc_start: 0.8604 (t80) cc_final: 0.8351 (t80) REVERT: R 78 ASN cc_start: 0.9099 (t0) cc_final: 0.8743 (t0) REVERT: R 147 ARG cc_start: 0.8862 (mmm-85) cc_final: 0.8251 (tpp80) REVERT: R 155 MET cc_start: 0.8714 (ttt) cc_final: 0.8412 (ttm) REVERT: R 183 MET cc_start: 0.8696 (mmm) cc_final: 0.8366 (tpp) REVERT: R 287 PHE cc_start: 0.9099 (t80) cc_final: 0.8853 (t80) REVERT: R 308 MET cc_start: 0.8807 (mmm) cc_final: 0.8254 (mmm) REVERT: R 310 ASN cc_start: 0.9270 (t0) cc_final: 0.8467 (t0) REVERT: R 317 MET cc_start: 0.8894 (mtp) cc_final: 0.8617 (mtp) outliers start: 16 outliers final: 8 residues processed: 243 average time/residue: 0.2042 time to fit residues: 67.8176 Evaluate side-chains 213 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 205 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 85 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 0.0470 chunk 48 optimal weight: 0.0980 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 86 optimal weight: 0.0050 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.116337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.100595 restraints weight = 16662.414| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.39 r_work: 0.3357 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8501 Z= 0.163 Angle : 0.599 9.115 11502 Z= 0.305 Chirality : 0.042 0.166 1276 Planarity : 0.004 0.047 1468 Dihedral : 5.082 57.959 1145 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.33 % Allowed : 17.28 % Favored : 80.40 % 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: -2.33 (0.25), residues: 1042 helix: 0.08 (0.27), residues: 367 sheet: -1.87 (0.35), residues: 198 loop : -2.76 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 278 PHE 0.027 0.001 PHE R 293 TYR 0.022 0.001 TYR R 178 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9070 (tt0) cc_final: 0.8786 (tt0) REVERT: A 24 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7574 (pp20) REVERT: A 194 MET cc_start: 0.8963 (mtt) cc_final: 0.8748 (ttm) REVERT: A 202 ASP cc_start: 0.8721 (t0) cc_final: 0.8476 (t0) REVERT: A 212 GLU cc_start: 0.8994 (tt0) cc_final: 0.8784 (tm-30) REVERT: A 240 GLN cc_start: 0.8862 (tp-100) cc_final: 0.8486 (tp-100) REVERT: A 267 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7938 (mmtm) REVERT: A 268 ASP cc_start: 0.6896 (m-30) cc_final: 0.6355 (p0) REVERT: A 302 GLN cc_start: 0.9324 (mm-40) cc_final: 0.8881 (mm-40) REVERT: A 319 MET cc_start: 0.7637 (mmm) cc_final: 0.7275 (mmm) REVERT: A 326 GLN cc_start: 0.8579 (mm110) cc_final: 0.8112 (mm110) REVERT: A 337 ASP cc_start: 0.9197 (t0) cc_final: 0.8798 (t0) REVERT: B 19 ARG cc_start: 0.7706 (tmt-80) cc_final: 0.6965 (ttm-80) REVERT: B 125 ASN cc_start: 0.8953 (t0) cc_final: 0.8490 (t0) REVERT: B 220 GLN cc_start: 0.8560 (mt0) cc_final: 0.8156 (tt0) REVERT: B 228 ASP cc_start: 0.8748 (m-30) cc_final: 0.8120 (m-30) REVERT: B 293 ASN cc_start: 0.7873 (t0) cc_final: 0.7520 (t0) REVERT: B 308 LEU cc_start: 0.9291 (mm) cc_final: 0.8837 (mp) REVERT: B 325 MET cc_start: 0.8766 (mmt) cc_final: 0.8566 (mmt) REVERT: B 333 ASP cc_start: 0.8473 (p0) cc_final: 0.8046 (p0) REVERT: B 339 TRP cc_start: 0.8886 (m100) cc_final: 0.8513 (m100) REVERT: G 46 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8172 (tp30) REVERT: N 32 TYR cc_start: 0.8409 (m-10) cc_final: 0.8108 (m-10) REVERT: N 76 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8246 (mptt) REVERT: N 77 ASN cc_start: 0.8178 (t0) cc_final: 0.7665 (t0) REVERT: N 108 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: N 123 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8492 (tp40) REVERT: R 60 TYR cc_start: 0.8649 (t80) cc_final: 0.8439 (t80) REVERT: R 78 ASN cc_start: 0.9149 (t0) cc_final: 0.8770 (t0) REVERT: R 86 MET cc_start: 0.8670 (mtp) cc_final: 0.8453 (mtp) REVERT: R 147 ARG cc_start: 0.8818 (mmm-85) cc_final: 0.8307 (tpp80) REVERT: R 155 MET cc_start: 0.8694 (ttt) cc_final: 0.8259 (mtp) REVERT: R 183 MET cc_start: 0.8785 (mmm) cc_final: 0.8441 (tpp) REVERT: R 308 MET cc_start: 0.8826 (mmm) cc_final: 0.8329 (mmm) REVERT: R 310 ASN cc_start: 0.9236 (t0) cc_final: 0.8455 (t0) REVERT: R 317 MET cc_start: 0.8821 (mtp) cc_final: 0.8591 (mtp) outliers start: 21 outliers final: 12 residues processed: 229 average time/residue: 0.1956 time to fit residues: 61.3468 Evaluate side-chains 215 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 72 optimal weight: 0.0970 chunk 19 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 81 optimal weight: 0.0470 chunk 87 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 278 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.116355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.100932 restraints weight = 16471.199| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.32 r_work: 0.3366 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8501 Z= 0.154 Angle : 0.580 7.195 11502 Z= 0.296 Chirality : 0.041 0.161 1276 Planarity : 0.004 0.045 1468 Dihedral : 4.779 58.227 1145 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.21 % Allowed : 19.05 % Favored : 77.74 % 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: -1.88 (0.26), residues: 1042 helix: 0.47 (0.28), residues: 374 sheet: -1.57 (0.36), residues: 199 loop : -2.57 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.005 0.001 HIS R 278 PHE 0.021 0.001 PHE R 287 TYR 0.017 0.001 TYR R 301 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9055 (tt0) cc_final: 0.8796 (tt0) REVERT: A 24 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7614 (pp20) REVERT: A 25 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8729 (mtmm) REVERT: A 194 MET cc_start: 0.8986 (mtt) cc_final: 0.8695 (ttm) REVERT: A 202 ASP cc_start: 0.8808 (t0) cc_final: 0.8517 (t0) REVERT: A 212 GLU cc_start: 0.9030 (tt0) cc_final: 0.8800 (tm-30) REVERT: A 240 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8372 (tp-100) REVERT: A 268 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6540 (p0) REVERT: A 302 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8821 (mm110) REVERT: A 326 GLN cc_start: 0.8642 (mm110) cc_final: 0.8173 (mm110) REVERT: B 19 ARG cc_start: 0.7681 (tmt-80) cc_final: 0.6909 (ttm-80) REVERT: B 125 ASN cc_start: 0.8988 (t0) cc_final: 0.8449 (t0) REVERT: B 215 GLU cc_start: 0.7420 (pt0) cc_final: 0.7168 (tm-30) REVERT: B 220 GLN cc_start: 0.8549 (mt0) cc_final: 0.8112 (tt0) REVERT: B 228 ASP cc_start: 0.8775 (m-30) cc_final: 0.8172 (m-30) REVERT: B 289 TYR cc_start: 0.7928 (m-10) cc_final: 0.7137 (m-10) REVERT: B 293 ASN cc_start: 0.7886 (t0) cc_final: 0.7262 (t0) REVERT: B 339 TRP cc_start: 0.8882 (m100) cc_final: 0.7497 (m-90) REVERT: G 42 ASP cc_start: 0.8587 (m-30) cc_final: 0.8286 (m-30) REVERT: G 46 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8245 (tp30) REVERT: G 55 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8530 (mmtm) REVERT: N 6 GLU cc_start: 0.7568 (mp0) cc_final: 0.6852 (mm-30) REVERT: N 73 ASP cc_start: 0.6744 (t0) cc_final: 0.6365 (t0) REVERT: N 76 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8053 (mppt) REVERT: N 77 ASN cc_start: 0.8234 (t0) cc_final: 0.7770 (t0) REVERT: N 123 GLN cc_start: 0.8900 (tp-100) cc_final: 0.8416 (tp40) REVERT: R 60 TYR cc_start: 0.8613 (t80) cc_final: 0.8387 (t80) REVERT: R 69 ARG cc_start: 0.8916 (mtm-85) cc_final: 0.8412 (mtt90) REVERT: R 78 ASN cc_start: 0.9131 (t0) cc_final: 0.8730 (t0) REVERT: R 147 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8233 (tpp80) REVERT: R 155 MET cc_start: 0.8713 (ttt) cc_final: 0.8262 (mtp) REVERT: R 183 MET cc_start: 0.8782 (mmm) cc_final: 0.8419 (tpp) REVERT: R 308 MET cc_start: 0.8859 (mmm) cc_final: 0.8394 (mmm) REVERT: R 310 ASN cc_start: 0.9252 (t0) cc_final: 0.8444 (t0) REVERT: R 317 MET cc_start: 0.8821 (mtp) cc_final: 0.8571 (mtp) outliers start: 29 outliers final: 17 residues processed: 243 average time/residue: 0.1921 time to fit residues: 64.2543 Evaluate side-chains 231 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS R 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.110851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093760 restraints weight = 17160.717| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.52 r_work: 0.3258 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8501 Z= 0.292 Angle : 0.654 8.209 11502 Z= 0.336 Chirality : 0.043 0.163 1276 Planarity : 0.004 0.044 1468 Dihedral : 4.901 50.211 1145 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.43 % Allowed : 22.04 % Favored : 74.53 % 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: -1.85 (0.26), residues: 1042 helix: 0.53 (0.28), residues: 379 sheet: -1.47 (0.37), residues: 194 loop : -2.68 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.020 0.002 PHE R 287 TYR 0.022 0.002 TYR A 283 ARG 0.007 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9098 (tt0) cc_final: 0.8851 (tt0) REVERT: A 24 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7612 (pp20) REVERT: A 25 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8730 (mtmm) REVERT: A 202 ASP cc_start: 0.8837 (t0) cc_final: 0.8528 (t0) REVERT: A 212 GLU cc_start: 0.9130 (tt0) cc_final: 0.8828 (tm-30) REVERT: A 240 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8369 (tp-100) REVERT: A 252 ASN cc_start: 0.8681 (p0) cc_final: 0.8455 (p0) REVERT: A 268 ASP cc_start: 0.7076 (m-30) cc_final: 0.6773 (p0) REVERT: A 302 GLN cc_start: 0.9346 (mm-40) cc_final: 0.8909 (mm110) REVERT: A 326 GLN cc_start: 0.8744 (mm110) cc_final: 0.8293 (mm110) REVERT: A 337 ASP cc_start: 0.9280 (t0) cc_final: 0.9071 (t0) REVERT: B 228 ASP cc_start: 0.8856 (m-30) cc_final: 0.8261 (m-30) REVERT: B 293 ASN cc_start: 0.8008 (t0) cc_final: 0.7537 (t0) REVERT: B 308 LEU cc_start: 0.9165 (mp) cc_final: 0.8821 (mt) REVERT: B 339 TRP cc_start: 0.8917 (m100) cc_final: 0.8606 (m100) REVERT: G 46 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8289 (tp30) REVERT: N 73 ASP cc_start: 0.6804 (t0) cc_final: 0.6370 (t0) REVERT: N 76 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8032 (mppt) REVERT: N 77 ASN cc_start: 0.8333 (t0) cc_final: 0.7844 (t0) REVERT: N 123 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8482 (tp-100) REVERT: R 30 TYR cc_start: 0.8281 (p90) cc_final: 0.7871 (p90) REVERT: R 60 TYR cc_start: 0.8652 (t80) cc_final: 0.8416 (t80) REVERT: R 78 ASN cc_start: 0.9185 (t0) cc_final: 0.8854 (t0) REVERT: R 147 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8365 (tpp80) REVERT: R 155 MET cc_start: 0.8830 (ttt) cc_final: 0.8525 (ttm) REVERT: R 183 MET cc_start: 0.8818 (mmm) cc_final: 0.8516 (tpp) REVERT: R 253 MET cc_start: 0.9322 (mmm) cc_final: 0.9110 (mmm) REVERT: R 308 MET cc_start: 0.8907 (mmm) cc_final: 0.8431 (mmm) REVERT: R 310 ASN cc_start: 0.9348 (t0) cc_final: 0.8534 (t0) REVERT: R 317 MET cc_start: 0.8852 (mtp) cc_final: 0.8517 (mtp) outliers start: 31 outliers final: 20 residues processed: 226 average time/residue: 0.1986 time to fit residues: 61.5658 Evaluate side-chains 210 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 70 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 0.0570 chunk 44 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.113744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097382 restraints weight = 16939.303| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.42 r_work: 0.3303 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8501 Z= 0.186 Angle : 0.622 9.854 11502 Z= 0.316 Chirality : 0.042 0.160 1276 Planarity : 0.004 0.046 1468 Dihedral : 4.821 56.649 1145 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.21 % Allowed : 22.81 % Favored : 73.98 % 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: -1.52 (0.26), residues: 1042 helix: 0.81 (0.28), residues: 376 sheet: -1.29 (0.37), residues: 191 loop : -2.45 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.002 0.001 HIS B 266 PHE 0.022 0.001 PHE R 287 TYR 0.030 0.002 TYR A 283 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9086 (tt0) cc_final: 0.8821 (tt0) REVERT: A 24 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7612 (pp20) REVERT: A 25 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8685 (mtmm) REVERT: A 202 ASP cc_start: 0.8818 (t0) cc_final: 0.8501 (t0) REVERT: A 212 GLU cc_start: 0.9071 (tt0) cc_final: 0.8796 (tm-30) REVERT: A 240 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8341 (tp-100) REVERT: A 252 ASN cc_start: 0.8658 (p0) cc_final: 0.8442 (p0) REVERT: A 268 ASP cc_start: 0.7052 (m-30) cc_final: 0.6713 (p0) REVERT: A 302 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8864 (mm110) REVERT: A 326 GLN cc_start: 0.8789 (mm110) cc_final: 0.8349 (mm110) REVERT: A 337 ASP cc_start: 0.9266 (t0) cc_final: 0.8947 (t0) REVERT: B 58 ILE cc_start: 0.8622 (pt) cc_final: 0.8391 (pt) REVERT: B 215 GLU cc_start: 0.7433 (pt0) cc_final: 0.7183 (tm-30) REVERT: B 220 GLN cc_start: 0.8540 (mt0) cc_final: 0.8117 (tt0) REVERT: B 228 ASP cc_start: 0.8858 (m-30) cc_final: 0.8366 (m-30) REVERT: B 264 TYR cc_start: 0.8877 (m-10) cc_final: 0.8620 (m-10) REVERT: B 289 TYR cc_start: 0.8119 (m-10) cc_final: 0.7428 (m-10) REVERT: B 293 ASN cc_start: 0.7982 (t0) cc_final: 0.7371 (t0) REVERT: B 339 TRP cc_start: 0.8909 (m100) cc_final: 0.8590 (m100) REVERT: G 42 ASP cc_start: 0.8609 (m-30) cc_final: 0.8293 (m-30) REVERT: G 46 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8293 (tp30) REVERT: N 73 ASP cc_start: 0.6667 (t0) cc_final: 0.6244 (t0) REVERT: N 76 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8031 (mppt) REVERT: N 77 ASN cc_start: 0.8308 (t0) cc_final: 0.7806 (t0) REVERT: R 30 TYR cc_start: 0.8180 (p90) cc_final: 0.7803 (p90) REVERT: R 60 TYR cc_start: 0.8624 (t80) cc_final: 0.8413 (t80) REVERT: R 78 ASN cc_start: 0.9151 (t0) cc_final: 0.8808 (t0) REVERT: R 147 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8213 (tpp80) REVERT: R 155 MET cc_start: 0.8729 (ttt) cc_final: 0.8380 (ttm) REVERT: R 183 MET cc_start: 0.8867 (mmm) cc_final: 0.8477 (tpp) REVERT: R 308 MET cc_start: 0.8879 (mmm) cc_final: 0.8463 (mmm) REVERT: R 310 ASN cc_start: 0.9332 (t0) cc_final: 0.8593 (t0) REVERT: R 317 MET cc_start: 0.8839 (mtp) cc_final: 0.8500 (mtp) outliers start: 29 outliers final: 22 residues processed: 230 average time/residue: 0.1896 time to fit residues: 60.5460 Evaluate side-chains 222 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 0.2980 chunk 102 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.115023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.098607 restraints weight = 16939.063| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.44 r_work: 0.3321 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8501 Z= 0.177 Angle : 0.629 9.211 11502 Z= 0.317 Chirality : 0.042 0.162 1276 Planarity : 0.003 0.046 1468 Dihedral : 4.740 54.910 1145 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.21 % Allowed : 22.81 % Favored : 73.98 % 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: -1.42 (0.26), residues: 1042 helix: 0.77 (0.28), residues: 381 sheet: -1.14 (0.37), residues: 189 loop : -2.36 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.001 0.001 HIS B 266 PHE 0.023 0.001 PHE R 293 TYR 0.025 0.002 TYR A 283 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9096 (tt0) cc_final: 0.8832 (tt0) REVERT: A 24 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7635 (pp20) REVERT: A 25 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8721 (mtmm) REVERT: A 202 ASP cc_start: 0.8850 (t0) cc_final: 0.8512 (t0) REVERT: A 212 GLU cc_start: 0.9041 (tt0) cc_final: 0.8763 (tm-30) REVERT: A 240 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8323 (tp-100) REVERT: A 268 ASP cc_start: 0.7080 (m-30) cc_final: 0.6761 (p0) REVERT: A 298 TYR cc_start: 0.8826 (t80) cc_final: 0.8235 (t80) REVERT: A 326 GLN cc_start: 0.8833 (mm110) cc_final: 0.8431 (mm110) REVERT: A 337 ASP cc_start: 0.9285 (t0) cc_final: 0.8952 (t0) REVERT: B 19 ARG cc_start: 0.7665 (tmt-80) cc_final: 0.6916 (ttm-80) REVERT: B 58 ILE cc_start: 0.8605 (pt) cc_final: 0.8368 (pt) REVERT: B 215 GLU cc_start: 0.7396 (pt0) cc_final: 0.7118 (tm-30) REVERT: B 220 GLN cc_start: 0.8539 (mt0) cc_final: 0.8104 (tt0) REVERT: B 228 ASP cc_start: 0.8857 (m-30) cc_final: 0.8367 (m-30) REVERT: B 289 TYR cc_start: 0.8081 (m-10) cc_final: 0.7319 (m-10) REVERT: B 293 ASN cc_start: 0.7997 (t0) cc_final: 0.7458 (t0) REVERT: B 308 LEU cc_start: 0.9171 (mp) cc_final: 0.8802 (mt) REVERT: B 333 ASP cc_start: 0.8513 (p0) cc_final: 0.8193 (p0) REVERT: B 339 TRP cc_start: 0.8913 (m100) cc_final: 0.8606 (m100) REVERT: G 17 MET cc_start: 0.6667 (mmm) cc_final: 0.6052 (mmp) REVERT: G 42 ASP cc_start: 0.8587 (m-30) cc_final: 0.8272 (m-30) REVERT: G 46 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8331 (tp30) REVERT: G 50 GLU cc_start: 0.8274 (mp0) cc_final: 0.7953 (mp0) REVERT: N 73 ASP cc_start: 0.6647 (t0) cc_final: 0.6234 (t0) REVERT: N 76 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8019 (mppt) REVERT: N 77 ASN cc_start: 0.8303 (t0) cc_final: 0.7869 (t0) REVERT: R 30 TYR cc_start: 0.8064 (p90) cc_final: 0.7722 (p90) REVERT: R 78 ASN cc_start: 0.9080 (t0) cc_final: 0.8802 (t0) REVERT: R 147 ARG cc_start: 0.8881 (mmm-85) cc_final: 0.8182 (tpp80) REVERT: R 155 MET cc_start: 0.8727 (ttt) cc_final: 0.8379 (ttm) REVERT: R 183 MET cc_start: 0.8859 (mmm) cc_final: 0.8466 (tpp) REVERT: R 236 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8467 (mm110) REVERT: R 310 ASN cc_start: 0.9323 (t0) cc_final: 0.8570 (t0) outliers start: 29 outliers final: 21 residues processed: 232 average time/residue: 0.1940 time to fit residues: 62.0224 Evaluate side-chains 220 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 chunk 33 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 80 optimal weight: 0.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.113736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.097348 restraints weight = 16948.691| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.42 r_work: 0.3302 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8501 Z= 0.209 Angle : 0.651 8.991 11502 Z= 0.329 Chirality : 0.043 0.161 1276 Planarity : 0.004 0.045 1468 Dihedral : 4.767 53.406 1145 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.32 % Allowed : 24.14 % Favored : 72.54 % 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: -1.32 (0.26), residues: 1042 helix: 0.82 (0.28), residues: 378 sheet: -0.98 (0.38), residues: 189 loop : -2.29 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.002 0.001 HIS B 266 PHE 0.025 0.001 PHE B 235 TYR 0.032 0.002 TYR R 60 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9106 (tt0) cc_final: 0.8863 (tt0) REVERT: A 24 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7538 (pp20) REVERT: A 25 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8671 (mtmm) REVERT: A 202 ASP cc_start: 0.8855 (t0) cc_final: 0.8494 (t0) REVERT: A 212 GLU cc_start: 0.9057 (tt0) cc_final: 0.8735 (tm-30) REVERT: A 240 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8300 (tp-100) REVERT: A 268 ASP cc_start: 0.7150 (m-30) cc_final: 0.6815 (p0) REVERT: A 298 TYR cc_start: 0.8855 (t80) cc_final: 0.8350 (t80) REVERT: A 319 MET cc_start: 0.8120 (mmm) cc_final: 0.7860 (tpp) REVERT: A 326 GLN cc_start: 0.8892 (mm110) cc_final: 0.8478 (mm110) REVERT: A 337 ASP cc_start: 0.9303 (t0) cc_final: 0.8976 (t0) REVERT: B 215 GLU cc_start: 0.7382 (pt0) cc_final: 0.7139 (tm-30) REVERT: B 220 GLN cc_start: 0.8549 (mt0) cc_final: 0.8106 (tt0) REVERT: B 228 ASP cc_start: 0.8858 (m-30) cc_final: 0.8352 (m-30) REVERT: B 289 TYR cc_start: 0.8131 (m-10) cc_final: 0.7416 (m-10) REVERT: B 293 ASN cc_start: 0.8027 (t0) cc_final: 0.7404 (t0) REVERT: B 308 LEU cc_start: 0.9163 (mp) cc_final: 0.8837 (mt) REVERT: B 339 TRP cc_start: 0.8917 (m100) cc_final: 0.8624 (m100) REVERT: G 17 MET cc_start: 0.6652 (mmm) cc_final: 0.6077 (mmp) REVERT: G 42 ASP cc_start: 0.8634 (m-30) cc_final: 0.8328 (m-30) REVERT: G 46 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8323 (tp30) REVERT: G 50 GLU cc_start: 0.8233 (mp0) cc_final: 0.7931 (mp0) REVERT: N 73 ASP cc_start: 0.6633 (t0) cc_final: 0.6211 (t0) REVERT: N 76 LYS cc_start: 0.8764 (mmmt) cc_final: 0.7915 (mppt) REVERT: N 77 ASN cc_start: 0.8344 (t0) cc_final: 0.7869 (t0) REVERT: N 123 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8842 (tp-100) REVERT: R 64 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8255 (mt0) REVERT: R 69 ARG cc_start: 0.8927 (mtm-85) cc_final: 0.8510 (mtm-85) REVERT: R 78 ASN cc_start: 0.9081 (t0) cc_final: 0.8797 (t0) REVERT: R 147 ARG cc_start: 0.8884 (mmm-85) cc_final: 0.8204 (tpp80) REVERT: R 155 MET cc_start: 0.8757 (ttt) cc_final: 0.8407 (ttm) REVERT: R 183 MET cc_start: 0.8864 (mmm) cc_final: 0.8459 (tpp) REVERT: R 236 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8440 (mm110) REVERT: R 310 ASN cc_start: 0.9323 (t0) cc_final: 0.8617 (t0) outliers start: 30 outliers final: 22 residues processed: 222 average time/residue: 0.2208 time to fit residues: 68.0423 Evaluate side-chains 218 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN R 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.114643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.098273 restraints weight = 16942.427| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.41 r_work: 0.3317 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 0.038 8501 Z= 0.188 Angle : 0.652 8.697 11502 Z= 0.327 Chirality : 0.043 0.176 1276 Planarity : 0.004 0.045 1468 Dihedral : 4.745 54.832 1145 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.55 % Allowed : 24.36 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.27), residues: 1042 helix: 0.89 (0.28), residues: 378 sheet: -0.86 (0.38), residues: 189 loop : -2.24 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 47 HIS 0.001 0.001 HIS B 266 PHE 0.026 0.001 PHE B 235 TYR 0.024 0.002 TYR R 60 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9082 (tt0) cc_final: 0.8858 (tt0) REVERT: A 202 ASP cc_start: 0.8861 (t0) cc_final: 0.8502 (t0) REVERT: A 212 GLU cc_start: 0.9075 (tt0) cc_final: 0.8781 (tm-30) REVERT: A 240 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8298 (tp-100) REVERT: A 268 ASP cc_start: 0.7261 (m-30) cc_final: 0.6927 (p0) REVERT: A 298 TYR cc_start: 0.8847 (t80) cc_final: 0.8475 (t80) REVERT: A 326 GLN cc_start: 0.8918 (mm110) cc_final: 0.8528 (mm110) REVERT: A 337 ASP cc_start: 0.9296 (t0) cc_final: 0.8963 (t0) REVERT: B 89 LYS cc_start: 0.8506 (mttp) cc_final: 0.8201 (mptt) REVERT: B 215 GLU cc_start: 0.7375 (pt0) cc_final: 0.7165 (tm-30) REVERT: B 220 GLN cc_start: 0.8544 (mt0) cc_final: 0.8092 (tt0) REVERT: B 228 ASP cc_start: 0.8847 (m-30) cc_final: 0.8377 (m-30) REVERT: B 289 TYR cc_start: 0.8052 (m-10) cc_final: 0.7274 (m-10) REVERT: B 293 ASN cc_start: 0.7955 (t0) cc_final: 0.7397 (t0) REVERT: B 308 LEU cc_start: 0.9176 (mp) cc_final: 0.8841 (mt) REVERT: B 333 ASP cc_start: 0.8489 (p0) cc_final: 0.8191 (p0) REVERT: B 339 TRP cc_start: 0.8894 (m100) cc_final: 0.8600 (m100) REVERT: G 17 MET cc_start: 0.6637 (mmm) cc_final: 0.6170 (mmp) REVERT: G 42 ASP cc_start: 0.8646 (m-30) cc_final: 0.8337 (m-30) REVERT: G 46 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8338 (tp30) REVERT: G 50 GLU cc_start: 0.8199 (mp0) cc_final: 0.7892 (mp0) REVERT: N 73 ASP cc_start: 0.6646 (t0) cc_final: 0.6239 (t0) REVERT: N 76 LYS cc_start: 0.8776 (mmmt) cc_final: 0.7928 (mppt) REVERT: N 77 ASN cc_start: 0.8352 (t0) cc_final: 0.7920 (t0) REVERT: N 83 MET cc_start: 0.7832 (mtm) cc_final: 0.7603 (ptp) REVERT: R 69 ARG cc_start: 0.8884 (mtm-85) cc_final: 0.8481 (mtt90) REVERT: R 78 ASN cc_start: 0.9082 (t0) cc_final: 0.8788 (t0) REVERT: R 147 ARG cc_start: 0.8892 (mmm-85) cc_final: 0.8208 (tpp80) REVERT: R 155 MET cc_start: 0.8741 (ttt) cc_final: 0.8397 (ttm) REVERT: R 183 MET cc_start: 0.8857 (mmm) cc_final: 0.8459 (tpp) REVERT: R 236 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8459 (mm110) REVERT: R 310 ASN cc_start: 0.9289 (t0) cc_final: 0.8589 (t0) outliers start: 23 outliers final: 21 residues processed: 215 average time/residue: 0.1893 time to fit residues: 56.1667 Evaluate side-chains 216 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 49 optimal weight: 0.2980 chunk 39 optimal weight: 0.4980 chunk 44 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.116766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100269 restraints weight = 16855.597| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.44 r_work: 0.3346 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8501 Z= 0.177 Angle : 0.663 8.664 11502 Z= 0.333 Chirality : 0.042 0.161 1276 Planarity : 0.004 0.045 1468 Dihedral : 4.719 56.990 1145 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.21 % Allowed : 25.14 % Favored : 72.65 % 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: -1.09 (0.27), residues: 1042 helix: 0.99 (0.28), residues: 376 sheet: -0.78 (0.38), residues: 191 loop : -2.18 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 47 HIS 0.003 0.001 HIS B 225 PHE 0.026 0.001 PHE R 287 TYR 0.022 0.002 TYR A 283 ARG 0.005 0.000 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9084 (tt0) cc_final: 0.8863 (tt0) REVERT: A 193 ARG cc_start: 0.8442 (mtp-110) cc_final: 0.7899 (mtp85) REVERT: A 202 ASP cc_start: 0.8874 (t0) cc_final: 0.8617 (t0) REVERT: A 212 GLU cc_start: 0.9034 (tt0) cc_final: 0.8752 (tm-30) REVERT: A 240 GLN cc_start: 0.8929 (tp-100) cc_final: 0.8272 (tp-100) REVERT: A 268 ASP cc_start: 0.7281 (m-30) cc_final: 0.6908 (p0) REVERT: A 298 TYR cc_start: 0.8863 (t80) cc_final: 0.8427 (t80) REVERT: A 326 GLN cc_start: 0.8949 (mm110) cc_final: 0.8550 (mm110) REVERT: A 337 ASP cc_start: 0.9293 (t0) cc_final: 0.8973 (t0) REVERT: B 89 LYS cc_start: 0.8383 (mttp) cc_final: 0.8154 (mptt) REVERT: B 157 ILE cc_start: 0.8619 (mt) cc_final: 0.7839 (tt) REVERT: B 215 GLU cc_start: 0.7330 (pt0) cc_final: 0.7114 (tm-30) REVERT: B 220 GLN cc_start: 0.8509 (mt0) cc_final: 0.8056 (tt0) REVERT: B 228 ASP cc_start: 0.8824 (m-30) cc_final: 0.8388 (m-30) REVERT: B 289 TYR cc_start: 0.7968 (m-10) cc_final: 0.7225 (m-10) REVERT: B 293 ASN cc_start: 0.7895 (t0) cc_final: 0.7327 (t0) REVERT: B 308 LEU cc_start: 0.9192 (mp) cc_final: 0.8852 (mt) REVERT: B 333 ASP cc_start: 0.8376 (p0) cc_final: 0.8096 (p0) REVERT: B 339 TRP cc_start: 0.8931 (m100) cc_final: 0.8605 (m100) REVERT: G 17 MET cc_start: 0.6574 (mmm) cc_final: 0.6160 (mmp) REVERT: G 42 ASP cc_start: 0.8673 (m-30) cc_final: 0.8362 (m-30) REVERT: G 46 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8079 (tp30) REVERT: N 73 ASP cc_start: 0.6687 (t0) cc_final: 0.6291 (t0) REVERT: N 76 LYS cc_start: 0.8803 (mmmt) cc_final: 0.7914 (mppt) REVERT: N 77 ASN cc_start: 0.8411 (t0) cc_final: 0.7886 (t0) REVERT: N 112 SER cc_start: 0.9141 (m) cc_final: 0.8750 (p) REVERT: R 78 ASN cc_start: 0.9048 (t0) cc_final: 0.8754 (t0) REVERT: R 147 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8157 (tpp80) REVERT: R 155 MET cc_start: 0.8717 (ttt) cc_final: 0.8369 (ttm) REVERT: R 183 MET cc_start: 0.8852 (mmm) cc_final: 0.8472 (tpp) REVERT: R 236 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8465 (mm110) REVERT: R 310 ASN cc_start: 0.9246 (t0) cc_final: 0.8565 (t0) outliers start: 20 outliers final: 17 residues processed: 224 average time/residue: 0.2342 time to fit residues: 72.1883 Evaluate side-chains 213 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN B 183 HIS R 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.112726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095583 restraints weight = 17401.124| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.55 r_work: 0.3280 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8501 Z= 0.258 Angle : 0.705 8.822 11502 Z= 0.356 Chirality : 0.044 0.162 1276 Planarity : 0.004 0.044 1468 Dihedral : 4.829 52.632 1145 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.77 % Allowed : 24.70 % Favored : 72.54 % 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: -1.18 (0.27), residues: 1042 helix: 0.96 (0.28), residues: 377 sheet: -0.86 (0.39), residues: 189 loop : -2.26 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP N 47 HIS 0.003 0.001 HIS B 54 PHE 0.030 0.002 PHE B 235 TYR 0.024 0.002 TYR R 60 ARG 0.005 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3777.62 seconds wall clock time: 66 minutes 29.77 seconds (3989.77 seconds total)