Starting phenix.real_space_refine on Wed Feb 12 22:57:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oya_20223/02_2025/6oya_20223.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oya_20223/02_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_20223/02_2025/6oya_20223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oya_20223/02_2025/6oya_20223.map" model { file = "/net/cci-nas-00/data/ceres_data/6oya_20223/02_2025/6oya_20223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oya_20223/02_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-5592/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: 5.25, per 1000 atoms: 0.63 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: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.87 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: 2.20 Time building geometry restraints manager: 2.41 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: 0.010 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- 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 : 0.964 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: 0.2238 time to fit residues: 80.5243 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 : 0.934 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.112067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.095511 restraints weight = 16540.288| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.53 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 : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9090 (tt0) cc_final: 0.8824 (tt0) REVERT: A 182 GLU cc_start: 0.8467 (tt0) cc_final: 0.8237 (tp30) REVERT: A 194 MET cc_start: 0.8871 (mtt) cc_final: 0.8181 (mtp) REVERT: A 212 GLU cc_start: 0.9031 (tt0) cc_final: 0.8792 (tm-30) REVERT: A 240 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8316 (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: 0.8680 (mm110) cc_final: 0.8271 (mm110) REVERT: A 337 ASP cc_start: 0.9341 (t0) cc_final: 0.8965 (t0) REVERT: B 17 GLN cc_start: 0.7810 (mt0) cc_final: 0.7553 (tm-30) REVERT: B 19 ARG cc_start: 0.7827 (tmt-80) cc_final: 0.6998 (ttm-80) REVERT: B 101 MET cc_start: 0.9032 (mmm) cc_final: 0.8767 (mmm) REVERT: B 125 ASN cc_start: 0.8940 (t0) cc_final: 0.8497 (t0) REVERT: B 186 ASP cc_start: 0.8299 (p0) cc_final: 0.7923 (p0) REVERT: B 228 ASP cc_start: 0.8825 (m-30) cc_final: 0.8095 (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: 0.8368 (mmt) REVERT: B 293 ASN cc_start: 0.7762 (t0) cc_final: 0.7356 (t0) REVERT: B 308 LEU cc_start: 0.9323 (mm) cc_final: 0.8961 (mp) REVERT: B 337 LYS cc_start: 0.8322 (mttt) cc_final: 0.8098 (mmtm) REVERT: B 339 TRP cc_start: 0.8876 (m100) cc_final: 0.8417 (m100) REVERT: G 65 LYS cc_start: 0.7871 (mttt) cc_final: 0.7636 (mttm) REVERT: N 22 CYS cc_start: 0.7784 (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: 0.8242 (t0) cc_final: 0.7705 (t0) REVERT: N 123 GLN cc_start: 0.8980 (tp-100) cc_final: 0.8418 (tp-100) REVERT: R 60 TYR cc_start: 0.8604 (t80) cc_final: 0.8352 (t80) REVERT: R 78 ASN cc_start: 0.9099 (t0) cc_final: 0.8743 (t0) REVERT: R 147 ARG cc_start: 0.8863 (mmm-85) cc_final: 0.8252 (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: 0.8808 (mmm) cc_final: 0.8255 (mmm) REVERT: R 310 ASN cc_start: 0.9270 (t0) cc_final: 0.8468 (t0) REVERT: R 317 MET cc_start: 0.8895 (mtp) cc_final: 0.8618 (mtp) outliers start: 16 outliers final: 8 residues processed: 243 average time/residue: 0.2058 time to fit residues: 68.1087 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 : 0.875 ------------------------------------------------------------------------------- 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: 1.9990 chunk 61 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.113951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.097251 restraints weight = 16976.263| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.45 r_work: 0.3293 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2090 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= 0.212 Angle : 0.616 9.382 11502 Z= 0.316 Chirality : 0.043 0.168 1276 Planarity : 0.004 0.046 1468 Dihedral : 5.158 52.958 1145 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.66 % Allowed : 17.17 % Favored : 80.18 % 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: -2.46 (0.25), residues: 1042 helix: -0.03 (0.27), residues: 374 sheet: -1.98 (0.34), residues: 208 loop : -2.85 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS R 278 PHE 0.026 0.001 PHE R 293 TYR 0.017 0.002 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 234 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.992 Fit side-chains revert: symmetry clash 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: 0.8827 (tt0) REVERT: A 24 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7570 (pp20) REVERT: A 194 MET cc_start: 0.9036 (mtt) cc_final: 0.8833 (ttm) REVERT: A 202 ASP cc_start: 0.8703 (t0) cc_final: 0.8472 (t0) REVERT: A 212 GLU cc_start: 0.9057 (tt0) cc_final: 0.8812 (tm-30) REVERT: A 240 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8502 (tp-100) REVERT: A 268 ASP cc_start: 0.6954 (m-30) cc_final: 0.6371 (p0) REVERT: A 302 GLN cc_start: 0.9376 (mm-40) cc_final: 0.8922 (mm110) REVERT: A 326 GLN cc_start: 0.8621 (mm110) cc_final: 0.8128 (mm110) REVERT: A 337 ASP cc_start: 0.9289 (t0) cc_final: 0.9026 (t0) REVERT: B 17 GLN cc_start: 0.7722 (mt0) cc_final: 0.7484 (tm-30) REVERT: B 19 ARG cc_start: 0.7718 (tmt-80) cc_final: 0.6948 (ttm-80) REVERT: B 220 GLN cc_start: 0.8621 (mt0) cc_final: 0.8193 (tt0) REVERT: B 235 PHE cc_start: 0.8967 (t80) cc_final: 0.8686 (t80) REVERT: B 293 ASN cc_start: 0.7935 (t0) cc_final: 0.7579 (t0) REVERT: B 308 LEU cc_start: 0.9296 (mm) cc_final: 0.8850 (mp) REVERT: B 325 MET cc_start: 0.8802 (mmt) cc_final: 0.8587 (mmt) REVERT: B 333 ASP cc_start: 0.8546 (p0) cc_final: 0.8140 (p0) REVERT: B 339 TRP cc_start: 0.8912 (m100) cc_final: 0.8585 (m100) REVERT: N 76 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8274 (mptt) REVERT: N 77 ASN cc_start: 0.8330 (t0) cc_final: 0.7779 (t0) REVERT: N 123 GLN cc_start: 0.9042 (tp-100) cc_final: 0.8512 (tp-100) REVERT: R 60 TYR cc_start: 0.8659 (t80) cc_final: 0.8435 (t80) REVERT: R 78 ASN cc_start: 0.9172 (t0) cc_final: 0.8843 (t0) REVERT: R 147 ARG cc_start: 0.8855 (mmm-85) cc_final: 0.8340 (tpp80) REVERT: R 155 MET cc_start: 0.8783 (ttt) cc_final: 0.8420 (ttm) REVERT: R 183 MET cc_start: 0.8813 (mmm) cc_final: 0.8461 (tpp) REVERT: R 308 MET cc_start: 0.8842 (mmm) cc_final: 0.8304 (mmm) REVERT: R 310 ASN cc_start: 0.9279 (t0) cc_final: 0.8516 (t0) REVERT: R 317 MET cc_start: 0.8838 (mtp) cc_final: 0.8613 (mtp) outliers start: 24 outliers final: 15 residues processed: 227 average time/residue: 0.2019 time to fit residues: 62.6608 Evaluate side-chains 214 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 37 ILE 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 67 ARG Chi-restraints excluded: chain N residue 108 PHE 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 85 PHE 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: 0.7980 chunk 47 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 6 GLN B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.114139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097621 restraints weight = 16892.159| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.42 r_work: 0.3301 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2392 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= 0.192 Angle : 0.600 7.822 11502 Z= 0.306 Chirality : 0.042 0.163 1276 Planarity : 0.004 0.045 1468 Dihedral : 4.958 55.541 1145 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.10 % Allowed : 19.60 % Favored : 77.30 % 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: -2.06 (0.26), residues: 1042 helix: 0.31 (0.27), residues: 376 sheet: -1.77 (0.35), residues: 208 loop : -2.63 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS R 278 PHE 0.020 0.001 PHE R 287 TYR 0.017 0.002 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 240 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.905 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: 0.9072 (tt0) cc_final: 0.8822 (tt0) REVERT: A 24 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7557 (pp20) REVERT: A 194 MET cc_start: 0.9107 (mtt) cc_final: 0.8780 (ttm) REVERT: A 202 ASP cc_start: 0.8760 (t0) cc_final: 0.8498 (t0) REVERT: A 212 GLU cc_start: 0.9063 (tt0) cc_final: 0.8814 (tm-30) REVERT: A 240 GLN cc_start: 0.8928 (tp-100) cc_final: 0.8357 (tp-100) REVERT: A 252 ASN cc_start: 0.8490 (p0) cc_final: 0.8208 (p0) REVERT: A 268 ASP cc_start: 0.6974 (m-30) cc_final: 0.6430 (p0) REVERT: A 302 GLN cc_start: 0.9339 (mm-40) cc_final: 0.8898 (mm110) REVERT: A 326 GLN cc_start: 0.8652 (mm110) cc_final: 0.8158 (mm110) REVERT: A 337 ASP cc_start: 0.9267 (t0) cc_final: 0.8986 (t0) REVERT: B 17 GLN cc_start: 0.7701 (mt0) cc_final: 0.7473 (tm-30) REVERT: B 19 ARG cc_start: 0.7747 (tmt-80) cc_final: 0.6997 (ttm-80) REVERT: B 235 PHE cc_start: 0.9019 (t80) cc_final: 0.8767 (t80) REVERT: B 293 ASN cc_start: 0.7968 (t0) cc_final: 0.7517 (t0) REVERT: B 308 LEU cc_start: 0.9288 (mm) cc_final: 0.8918 (mp) REVERT: B 325 MET cc_start: 0.8798 (mmt) cc_final: 0.8597 (mmt) REVERT: B 339 TRP cc_start: 0.8913 (m100) cc_final: 0.8620 (m100) REVERT: G 46 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8235 (tp30) REVERT: N 6 GLU cc_start: 0.7766 (mp0) cc_final: 0.7089 (mm-30) REVERT: N 76 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8262 (mptt) REVERT: N 77 ASN cc_start: 0.8266 (t0) cc_final: 0.7785 (t0) REVERT: N 123 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8494 (tp-100) REVERT: R 60 TYR cc_start: 0.8662 (t80) cc_final: 0.8426 (t80) REVERT: R 78 ASN cc_start: 0.9167 (t0) cc_final: 0.8843 (t0) REVERT: R 147 ARG cc_start: 0.8888 (mmm-85) cc_final: 0.8366 (tpp80) REVERT: R 155 MET cc_start: 0.8778 (ttt) cc_final: 0.8325 (mtp) REVERT: R 183 MET cc_start: 0.8815 (mmm) cc_final: 0.8438 (tpp) REVERT: R 308 MET cc_start: 0.8840 (mmm) cc_final: 0.8358 (mmm) REVERT: R 310 ASN cc_start: 0.9300 (t0) cc_final: 0.8496 (t0) REVERT: R 317 MET cc_start: 0.8803 (mtp) cc_final: 0.8490 (mtp) outliers start: 28 outliers final: 18 residues processed: 233 average time/residue: 0.2158 time to fit residues: 68.0351 Evaluate side-chains 215 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 37 ILE 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 28 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 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 85 PHE 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: 5.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.3980 chunk 17 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.112811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096373 restraints weight = 16958.867| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.40 r_work: 0.3286 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8501 Z= 0.218 Angle : 0.622 9.336 11502 Z= 0.316 Chirality : 0.042 0.165 1276 Planarity : 0.004 0.046 1468 Dihedral : 4.916 54.562 1145 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.65 % Allowed : 20.27 % Favored : 76.08 % 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: -1.89 (0.26), residues: 1042 helix: 0.52 (0.27), residues: 375 sheet: -1.57 (0.36), residues: 207 loop : -2.65 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS R 278 PHE 0.021 0.001 PHE R 287 TYR 0.020 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 234 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.051 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: 0.8842 (tt0) REVERT: A 24 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7580 (pp20) REVERT: A 202 ASP cc_start: 0.8792 (t0) cc_final: 0.8482 (t0) REVERT: A 212 GLU cc_start: 0.9101 (tt0) cc_final: 0.8823 (tm-30) REVERT: A 240 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8356 (tp-100) REVERT: A 268 ASP cc_start: 0.6994 (m-30) cc_final: 0.6626 (p0) REVERT: A 302 GLN cc_start: 0.9335 (mm-40) cc_final: 0.8906 (mm110) REVERT: A 326 GLN cc_start: 0.8694 (mm110) cc_final: 0.8230 (mm110) REVERT: B 17 GLN cc_start: 0.7717 (mt0) cc_final: 0.7496 (tm-30) REVERT: B 19 ARG cc_start: 0.7770 (tmt-80) cc_final: 0.6981 (ttm-80) REVERT: B 58 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8623 (pt) REVERT: B 215 GLU cc_start: 0.7427 (pt0) cc_final: 0.7201 (tm-30) REVERT: B 235 PHE cc_start: 0.9023 (t80) cc_final: 0.8763 (t80) REVERT: B 243 THR cc_start: 0.8833 (p) cc_final: 0.8628 (p) REVERT: B 264 TYR cc_start: 0.8810 (m-10) cc_final: 0.8571 (m-10) REVERT: B 289 TYR cc_start: 0.8098 (m-10) cc_final: 0.7404 (m-10) REVERT: B 293 ASN cc_start: 0.7932 (t0) cc_final: 0.7319 (t0) REVERT: B 308 LEU cc_start: 0.9279 (mm) cc_final: 0.8908 (mp) REVERT: B 339 TRP cc_start: 0.8914 (m100) cc_final: 0.8629 (m100) REVERT: G 46 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8317 (tp30) REVERT: N 76 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8283 (mptt) REVERT: N 77 ASN cc_start: 0.8313 (t0) cc_final: 0.7761 (t0) REVERT: N 123 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8504 (tp-100) REVERT: R 60 TYR cc_start: 0.8654 (t80) cc_final: 0.8423 (t80) REVERT: R 78 ASN cc_start: 0.9165 (t0) cc_final: 0.8846 (t0) REVERT: R 147 ARG cc_start: 0.8905 (mmm-85) cc_final: 0.8346 (tpp80) REVERT: R 155 MET cc_start: 0.8797 (ttt) cc_final: 0.8491 (ttm) REVERT: R 183 MET cc_start: 0.8809 (mmm) cc_final: 0.8424 (tpp) REVERT: R 308 MET cc_start: 0.8838 (mmm) cc_final: 0.8331 (mmm) REVERT: R 310 ASN cc_start: 0.9294 (t0) cc_final: 0.8523 (t0) REVERT: R 317 MET cc_start: 0.8809 (mtp) cc_final: 0.8484 (mtp) outliers start: 33 outliers final: 23 residues processed: 225 average time/residue: 0.1951 time to fit residues: 60.4352 Evaluate side-chains 217 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 37 ILE Chi-restraints excluded: chain B residue 58 ILE 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 268 ASN 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 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 67 ARG Chi-restraints excluded: chain N residue 108 PHE 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 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: 0.2980 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 chunk 5 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.113834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.098211 restraints weight = 16664.072| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.33 r_work: 0.3323 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8501 Z= 0.173 Angle : 0.611 8.532 11502 Z= 0.312 Chirality : 0.042 0.176 1276 Planarity : 0.004 0.046 1468 Dihedral : 4.856 57.377 1145 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.43 % Allowed : 21.82 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.63 (0.26), residues: 1042 helix: 0.67 (0.28), residues: 378 sheet: -1.43 (0.36), residues: 204 loop : -2.46 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS B 183 PHE 0.021 0.001 PHE R 287 TYR 0.031 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 242 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9047 (tt0) cc_final: 0.8815 (tt0) REVERT: A 24 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7607 (pp20) REVERT: A 202 ASP cc_start: 0.8794 (t0) cc_final: 0.8460 (t0) REVERT: A 212 GLU cc_start: 0.9062 (tt0) cc_final: 0.8802 (tm-30) REVERT: A 240 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8334 (tp-100) REVERT: A 268 ASP cc_start: 0.6969 (m-30) cc_final: 0.6514 (p0) REVERT: A 302 GLN cc_start: 0.9286 (mm-40) cc_final: 0.8853 (mm110) REVERT: A 319 MET cc_start: 0.8058 (mmm) cc_final: 0.7746 (tmm) REVERT: A 326 GLN cc_start: 0.8699 (mm110) cc_final: 0.8231 (mm110) REVERT: A 337 ASP cc_start: 0.9160 (t0) cc_final: 0.8887 (t0) REVERT: B 19 ARG cc_start: 0.7724 (tmt-80) cc_final: 0.7055 (ttm-80) REVERT: B 57 LYS cc_start: 0.8928 (ptpp) cc_final: 0.8483 (ptmm) REVERT: B 58 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8571 (pt) REVERT: B 89 LYS cc_start: 0.8612 (mttp) cc_final: 0.8326 (mptt) REVERT: B 215 GLU cc_start: 0.7405 (pt0) cc_final: 0.7201 (tm-30) REVERT: B 220 GLN cc_start: 0.8554 (mt0) cc_final: 0.8122 (tt0) REVERT: B 243 THR cc_start: 0.8822 (p) cc_final: 0.8607 (p) REVERT: B 251 ARG cc_start: 0.8566 (mtt180) cc_final: 0.8331 (mtp180) REVERT: B 289 TYR cc_start: 0.8055 (m-10) cc_final: 0.7376 (m-10) REVERT: B 293 ASN cc_start: 0.7978 (t0) cc_final: 0.7345 (t0) REVERT: B 308 LEU cc_start: 0.9258 (mm) cc_final: 0.8948 (mp) REVERT: B 339 TRP cc_start: 0.8924 (m100) cc_final: 0.8639 (m100) REVERT: G 46 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8316 (tp30) REVERT: N 73 ASP cc_start: 0.6669 (t0) cc_final: 0.6261 (t0) REVERT: N 76 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8033 (mppt) REVERT: N 77 ASN cc_start: 0.8283 (t0) cc_final: 0.7828 (t0) REVERT: R 60 TYR cc_start: 0.8625 (t80) cc_final: 0.8423 (t80) REVERT: R 78 ASN cc_start: 0.9130 (t0) cc_final: 0.8780 (t0) REVERT: R 147 ARG cc_start: 0.8856 (mmm-85) cc_final: 0.8215 (tpp80) REVERT: R 155 MET cc_start: 0.8728 (ttt) cc_final: 0.8381 (ttm) REVERT: R 183 MET cc_start: 0.8776 (mmm) cc_final: 0.8366 (tpp) REVERT: R 308 MET cc_start: 0.8803 (mmm) cc_final: 0.8357 (mmm) REVERT: R 310 ASN cc_start: 0.9250 (t0) cc_final: 0.8489 (t0) REVERT: R 317 MET cc_start: 0.8790 (mtp) cc_final: 0.8459 (mtp) outliers start: 31 outliers final: 21 residues processed: 232 average time/residue: 0.2116 time to fit residues: 68.7394 Evaluate side-chains 215 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 270 ILE 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 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 108 PHE 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 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: 0.0980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.112130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.095852 restraints weight = 17111.164| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.40 r_work: 0.3278 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8501 Z= 0.243 Angle : 0.652 8.584 11502 Z= 0.333 Chirality : 0.044 0.172 1276 Planarity : 0.004 0.047 1468 Dihedral : 4.889 52.036 1145 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.10 % Allowed : 21.82 % Favored : 74.09 % 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: -1.57 (0.26), residues: 1042 helix: 0.71 (0.28), residues: 379 sheet: -1.31 (0.36), residues: 200 loop : -2.48 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 47 HIS 0.006 0.001 HIS R 278 PHE 0.025 0.002 PHE R 287 TYR 0.027 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 235 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9110 (tt0) cc_final: 0.8874 (tt0) REVERT: A 202 ASP cc_start: 0.8870 (t0) cc_final: 0.8535 (t0) REVERT: A 212 GLU cc_start: 0.9101 (tt0) cc_final: 0.8761 (tm-30) REVERT: A 240 GLN cc_start: 0.9009 (tp-100) cc_final: 0.8372 (tp-100) REVERT: A 268 ASP cc_start: 0.7047 (m-30) cc_final: 0.6572 (p0) REVERT: A 298 TYR cc_start: 0.8860 (t80) cc_final: 0.8359 (t80) REVERT: A 326 GLN cc_start: 0.8734 (mm110) cc_final: 0.8256 (mm110) REVERT: A 337 ASP cc_start: 0.9247 (t0) cc_final: 0.8961 (t0) REVERT: B 19 ARG cc_start: 0.7712 (tmt-80) cc_final: 0.6918 (ttm-80) REVERT: B 57 LYS cc_start: 0.9053 (ptpp) cc_final: 0.8628 (ptmm) REVERT: B 58 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8664 (pt) REVERT: B 215 GLU cc_start: 0.7390 (pt0) cc_final: 0.7171 (tm-30) REVERT: B 226 GLU cc_start: 0.8221 (mp0) cc_final: 0.8008 (mp0) REVERT: B 228 ASP cc_start: 0.8863 (m-30) cc_final: 0.8225 (m-30) REVERT: B 243 THR cc_start: 0.8910 (p) cc_final: 0.8707 (p) REVERT: B 293 ASN cc_start: 0.8066 (t0) cc_final: 0.7587 (t0) REVERT: B 308 LEU cc_start: 0.9237 (mm) cc_final: 0.8997 (mp) REVERT: B 339 TRP cc_start: 0.8921 (m100) cc_final: 0.8657 (m100) REVERT: G 17 MET cc_start: 0.6528 (mmm) cc_final: 0.6270 (mmp) REVERT: N 73 ASP cc_start: 0.6693 (t0) cc_final: 0.6263 (t0) REVERT: N 76 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8046 (mppt) REVERT: N 77 ASN cc_start: 0.8421 (t0) cc_final: 0.7977 (t0) REVERT: N 108 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: R 30 TYR cc_start: 0.7956 (p90) cc_final: 0.7573 (p90) REVERT: R 60 TYR cc_start: 0.8612 (t80) cc_final: 0.8248 (t80) REVERT: R 64 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.7769 (mt0) REVERT: R 69 ARG cc_start: 0.8918 (mtm-85) cc_final: 0.8573 (mtm-85) REVERT: R 78 ASN cc_start: 0.9158 (t0) cc_final: 0.8897 (t0) REVERT: R 147 ARG cc_start: 0.8892 (mmm-85) cc_final: 0.8268 (tpp80) REVERT: R 155 MET cc_start: 0.8827 (ttt) cc_final: 0.8490 (ttm) REVERT: R 183 MET cc_start: 0.8787 (mmm) cc_final: 0.8379 (tpp) REVERT: R 308 MET cc_start: 0.8921 (mmm) cc_final: 0.8477 (mmm) REVERT: R 310 ASN cc_start: 0.9302 (t0) cc_final: 0.8560 (t0) REVERT: R 317 MET cc_start: 0.8870 (mtp) cc_final: 0.8539 (mtp) outliers start: 37 outliers final: 23 residues processed: 224 average time/residue: 0.1996 time to fit residues: 61.0915 Evaluate side-chains 217 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 37 ILE Chi-restraints excluded: chain B residue 58 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 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 108 PHE 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 67 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 3 optimal weight: 0.0030 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.113522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.098243 restraints weight = 16709.836| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.33 r_work: 0.3321 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2914 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= 0.187 Angle : 0.640 10.052 11502 Z= 0.326 Chirality : 0.043 0.168 1276 Planarity : 0.004 0.050 1468 Dihedral : 4.866 55.939 1145 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.88 % Allowed : 23.92 % Favored : 73.20 % 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: -1.34 (0.27), residues: 1042 helix: 0.79 (0.28), residues: 374 sheet: -1.07 (0.38), residues: 195 loop : -2.24 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 47 HIS 0.005 0.001 HIS B 183 PHE 0.024 0.001 PHE R 287 TYR 0.025 0.002 TYR A 283 ARG 0.005 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 225 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9084 (tt0) cc_final: 0.8829 (tt0) REVERT: A 24 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7596 (pp20) REVERT: A 202 ASP cc_start: 0.8853 (t0) cc_final: 0.8515 (t0) REVERT: A 212 GLU cc_start: 0.9033 (tt0) cc_final: 0.8744 (tm-30) REVERT: A 240 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8340 (tp-100) REVERT: A 268 ASP cc_start: 0.6905 (m-30) cc_final: 0.6438 (p0) REVERT: A 298 TYR cc_start: 0.8828 (t80) cc_final: 0.8191 (t80) REVERT: A 326 GLN cc_start: 0.8777 (mm110) cc_final: 0.8332 (mm110) REVERT: A 337 ASP cc_start: 0.9238 (t0) cc_final: 0.8955 (t0) REVERT: B 19 ARG cc_start: 0.7682 (tmt-80) cc_final: 0.6923 (ttm-80) REVERT: B 57 LYS cc_start: 0.8924 (ptpp) cc_final: 0.8482 (ptmm) REVERT: B 58 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8649 (pt) REVERT: B 220 GLN cc_start: 0.8585 (mt0) cc_final: 0.8135 (tt0) REVERT: B 228 ASP cc_start: 0.8834 (m-30) cc_final: 0.8350 (m-30) REVERT: B 289 TYR cc_start: 0.8013 (m-10) cc_final: 0.7335 (m-10) REVERT: B 293 ASN cc_start: 0.7994 (t0) cc_final: 0.7385 (t0) REVERT: B 308 LEU cc_start: 0.9239 (mm) cc_final: 0.8968 (mp) REVERT: B 333 ASP cc_start: 0.8553 (p0) cc_final: 0.8262 (p0) REVERT: B 339 TRP cc_start: 0.8913 (m100) cc_final: 0.8644 (m100) REVERT: G 17 MET cc_start: 0.6632 (mmm) cc_final: 0.6001 (mmp) REVERT: G 46 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8321 (tp30) REVERT: N 77 ASN cc_start: 0.8376 (t0) cc_final: 0.7882 (t0) REVERT: N 123 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8853 (tp-100) REVERT: R 60 TYR cc_start: 0.8599 (t80) cc_final: 0.8258 (t80) REVERT: R 64 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: R 69 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8489 (mtm-85) REVERT: R 78 ASN cc_start: 0.9101 (t0) cc_final: 0.8817 (t0) REVERT: R 147 ARG cc_start: 0.8828 (mmm-85) cc_final: 0.8182 (tpp80) REVERT: R 155 MET cc_start: 0.8777 (ttt) cc_final: 0.8434 (ttm) REVERT: R 183 MET cc_start: 0.8758 (mmm) cc_final: 0.8350 (tpp) REVERT: R 257 MET cc_start: 0.7844 (mtm) cc_final: 0.7072 (mtp) REVERT: R 308 MET cc_start: 0.8898 (mmm) cc_final: 0.8439 (mmm) REVERT: R 310 ASN cc_start: 0.9267 (t0) cc_final: 0.8524 (t0) REVERT: R 317 MET cc_start: 0.8846 (mtp) cc_final: 0.8504 (mtp) outliers start: 26 outliers final: 20 residues processed: 217 average time/residue: 0.2046 time to fit residues: 60.7480 Evaluate side-chains 214 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 37 ILE Chi-restraints excluded: chain B residue 58 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 28 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 22 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 69 optimal weight: 0.0030 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 26 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.114358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098198 restraints weight = 16713.180| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.34 r_work: 0.3215 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3042 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= 0.176 Angle : 0.639 9.206 11502 Z= 0.324 Chirality : 0.043 0.167 1276 Planarity : 0.004 0.048 1468 Dihedral : 4.746 56.220 1145 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.55 % Allowed : 24.25 % Favored : 73.20 % 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: -1.12 (0.27), residues: 1042 helix: 1.00 (0.28), residues: 367 sheet: -0.94 (0.38), residues: 197 loop : -2.10 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 47 HIS 0.006 0.001 HIS B 225 PHE 0.025 0.001 PHE R 287 TYR 0.023 0.002 TYR A 283 ARG 0.005 0.000 ARG N 72 *********************** 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 224 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9079 (tt0) cc_final: 0.8858 (tt0) REVERT: A 202 ASP cc_start: 0.8811 (t0) cc_final: 0.8415 (t0) REVERT: A 212 GLU cc_start: 0.8983 (tt0) cc_final: 0.8729 (tm-30) REVERT: A 240 GLN cc_start: 0.8781 (tp-100) cc_final: 0.8090 (tp-100) REVERT: A 268 ASP cc_start: 0.6985 (m-30) cc_final: 0.6571 (p0) REVERT: A 298 TYR cc_start: 0.8859 (t80) cc_final: 0.8492 (t80) REVERT: A 326 GLN cc_start: 0.8810 (mm110) cc_final: 0.8367 (mm110) REVERT: A 337 ASP cc_start: 0.9379 (t0) cc_final: 0.9044 (t0) REVERT: B 58 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (pt) REVERT: B 215 GLU cc_start: 0.7747 (pt0) cc_final: 0.7347 (tm-30) REVERT: B 220 GLN cc_start: 0.8521 (mt0) cc_final: 0.7920 (tt0) REVERT: B 226 GLU cc_start: 0.8155 (mp0) cc_final: 0.7880 (mp0) REVERT: B 228 ASP cc_start: 0.8844 (m-30) cc_final: 0.8154 (m-30) REVERT: B 289 TYR cc_start: 0.7915 (m-10) cc_final: 0.7077 (m-10) REVERT: B 293 ASN cc_start: 0.7891 (t0) cc_final: 0.7283 (t0) REVERT: B 308 LEU cc_start: 0.9244 (mm) cc_final: 0.8976 (mp) REVERT: B 333 ASP cc_start: 0.8415 (p0) cc_final: 0.8169 (p0) REVERT: B 339 TRP cc_start: 0.8876 (m100) cc_final: 0.8566 (m100) REVERT: G 17 MET cc_start: 0.6389 (mmm) cc_final: 0.5923 (mmp) REVERT: G 42 ASP cc_start: 0.8717 (m-30) cc_final: 0.8405 (m-30) REVERT: G 46 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8075 (tp30) REVERT: N 76 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8387 (mppt) REVERT: N 77 ASN cc_start: 0.8288 (t0) cc_final: 0.7711 (t0) REVERT: N 83 MET cc_start: 0.7731 (mtm) cc_final: 0.7528 (ptp) REVERT: R 60 TYR cc_start: 0.8485 (t80) cc_final: 0.8235 (t80) REVERT: R 64 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7706 (mt0) REVERT: R 69 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8415 (mtm-85) REVERT: R 78 ASN cc_start: 0.8986 (t0) cc_final: 0.8714 (t0) REVERT: R 147 ARG cc_start: 0.8862 (mmm-85) cc_final: 0.8050 (tpp80) REVERT: R 155 MET cc_start: 0.8646 (ttt) cc_final: 0.8270 (ttm) REVERT: R 183 MET cc_start: 0.8621 (mmm) cc_final: 0.8200 (tpp) REVERT: R 310 ASN cc_start: 0.9285 (t0) cc_final: 0.8437 (t0) REVERT: R 317 MET cc_start: 0.8963 (mtp) cc_final: 0.8692 (ttp) outliers start: 23 outliers final: 18 residues processed: 216 average time/residue: 0.2086 time to fit residues: 62.0831 Evaluate side-chains 216 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 58 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** R 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.110382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094219 restraints weight = 16692.648| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.33 r_work: 0.3153 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3091 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= 0.269 Angle : 0.707 9.858 11502 Z= 0.357 Chirality : 0.044 0.167 1276 Planarity : 0.004 0.051 1468 Dihedral : 4.868 50.190 1145 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.77 % Allowed : 24.92 % Favored : 72.31 % 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: -1.28 (0.27), residues: 1042 helix: 0.88 (0.28), residues: 373 sheet: -1.02 (0.38), residues: 199 loop : -2.25 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 47 HIS 0.008 0.001 HIS B 225 PHE 0.028 0.002 PHE R 287 TYR 0.021 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 219 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9075 (tt0) cc_final: 0.8872 (tt0) REVERT: A 202 ASP cc_start: 0.8854 (t0) cc_final: 0.8425 (t0) REVERT: A 212 GLU cc_start: 0.9091 (tt0) cc_final: 0.8701 (tm-30) REVERT: A 240 GLN cc_start: 0.8800 (tp-100) cc_final: 0.8102 (tp-100) REVERT: A 268 ASP cc_start: 0.7060 (m-30) cc_final: 0.6628 (p0) REVERT: A 298 TYR cc_start: 0.8935 (t80) cc_final: 0.8693 (t80) REVERT: A 307 ASN cc_start: 0.8437 (t0) cc_final: 0.8195 (t0) REVERT: A 326 GLN cc_start: 0.8862 (mm110) cc_final: 0.8429 (mm110) REVERT: A 337 ASP cc_start: 0.9415 (t0) cc_final: 0.9088 (t0) REVERT: B 58 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8540 (pt) REVERT: B 215 GLU cc_start: 0.7627 (pt0) cc_final: 0.7286 (tm-30) REVERT: B 226 GLU cc_start: 0.8244 (mp0) cc_final: 0.7964 (mp0) REVERT: B 228 ASP cc_start: 0.8893 (m-30) cc_final: 0.7968 (m-30) REVERT: B 289 TYR cc_start: 0.7935 (m-10) cc_final: 0.7170 (m-10) REVERT: B 293 ASN cc_start: 0.7938 (t0) cc_final: 0.7242 (t0) REVERT: B 308 LEU cc_start: 0.9235 (mm) cc_final: 0.9020 (mp) REVERT: B 339 TRP cc_start: 0.8869 (m100) cc_final: 0.8568 (m100) REVERT: G 17 MET cc_start: 0.6405 (mmm) cc_final: 0.5908 (mmp) REVERT: N 76 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8465 (mppt) REVERT: N 77 ASN cc_start: 0.8411 (t0) cc_final: 0.7892 (t0) REVERT: N 83 MET cc_start: 0.7831 (mtm) cc_final: 0.7609 (ptp) REVERT: R 60 TYR cc_start: 0.8448 (t80) cc_final: 0.8066 (t80) REVERT: R 64 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7734 (mt0) REVERT: R 69 ARG cc_start: 0.8669 (mtm-85) cc_final: 0.8356 (mtm-85) REVERT: R 78 ASN cc_start: 0.9034 (t0) cc_final: 0.8771 (t0) REVERT: R 147 ARG cc_start: 0.8936 (mmm-85) cc_final: 0.8090 (tpp80) REVERT: R 155 MET cc_start: 0.8728 (ttt) cc_final: 0.8360 (ttm) REVERT: R 183 MET cc_start: 0.8615 (mmm) cc_final: 0.8187 (tpp) REVERT: R 253 MET cc_start: 0.9142 (mmm) cc_final: 0.8942 (mmm) REVERT: R 310 ASN cc_start: 0.9292 (t0) cc_final: 0.8423 (t0) outliers start: 25 outliers final: 18 residues processed: 210 average time/residue: 0.2005 time to fit residues: 58.4412 Evaluate side-chains 209 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 58 ILE 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 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 86 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.097222 restraints weight = 16856.240| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.33 r_work: 0.3191 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8501 Z= 0.201 Angle : 0.695 11.715 11502 Z= 0.348 Chirality : 0.044 0.168 1276 Planarity : 0.004 0.047 1468 Dihedral : 4.898 54.687 1145 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.44 % Allowed : 25.36 % Favored : 72.20 % 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: -1.10 (0.27), residues: 1042 helix: 1.04 (0.28), residues: 364 sheet: -0.94 (0.37), residues: 199 loop : -2.08 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP N 47 HIS 0.007 0.001 HIS B 225 PHE 0.027 0.001 PHE R 287 TYR 0.020 0.002 TYR A 283 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: 3782.27 seconds wall clock time: 68 minutes 5.25 seconds (4085.25 seconds total)