Starting phenix.real_space_refine on Wed Feb 12 18:07:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ioc_35615/02_2025/8ioc_35615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ioc_35615/02_2025/8ioc_35615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ioc_35615/02_2025/8ioc_35615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ioc_35615/02_2025/8ioc_35615.map" model { file = "/net/cci-nas-00/data/ceres_data/8ioc_35615/02_2025/8ioc_35615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ioc_35615/02_2025/8ioc_35615.cif" } resolution = 2.86 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= -0.001 sd= 0.017 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 67 5.16 5 C 5219 2.51 5 N 1422 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8223 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "R" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2158 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain breaks: 1 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "L" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 107 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.96, per 1000 atoms: 0.60 Number of scatterers: 8223 At special positions: 0 Unit cell: (84.609, 98.532, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 67 16.00 O 1514 8.00 N 1422 7.00 C 5219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 35 " - pdb=" SG CYS R 276 " distance=2.03 Simple disulfide: pdb=" SG CYS R 268 " - pdb=" SG CYS R 274 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 40.4% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.867A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.802A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.674A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.587A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.558A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.613A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 35' Processing helix chain 'R' and resid 41 through 65 removed outlier: 4.148A pdb=" N PHE R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 103 removed outlier: 3.702A pdb=" N PHE R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE R 76 " --> pdb=" O PRO R 72 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU R 77 " --> pdb=" O MET R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 148 removed outlier: 3.730A pdb=" N ILE R 113 " --> pdb=" O GLU R 109 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN R 114 " --> pdb=" O ASP R 110 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS R 115 " --> pdb=" O GLN R 111 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE R 119 " --> pdb=" O HIS R 115 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE R 120 " --> pdb=" O MET R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 155 Processing helix chain 'R' and resid 157 through 182 removed outlier: 3.505A pdb=" N TYR R 182 " --> pdb=" O VAL R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 223 removed outlier: 4.473A pdb=" N ILE R 189 " --> pdb=" O SER R 185 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL R 190 " --> pdb=" O LYS R 186 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET R 203 " --> pdb=" O MET R 199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA R 223 " --> pdb=" O LYS R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 268 removed outlier: 3.932A pdb=" N PHE R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) Proline residue: R 257 - end of helix Processing helix chain 'R' and resid 271 through 279 removed outlier: 4.120A pdb=" N CYS R 276 " --> pdb=" O PRO R 272 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR R 277 " --> pdb=" O TYR R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 299 removed outlier: 3.889A pdb=" N TYR R 284 " --> pdb=" O HIS R 280 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 303 through 313 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.771A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 39 through 45 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.523A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.828A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.422A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.601A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.810A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.817A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.877A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.911A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.030A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.927A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.695A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1167 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: 2.40 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1413 1.32 - 1.45: 2263 1.45 - 1.57: 4616 1.57 - 1.69: 0 1.69 - 1.82: 97 Bond restraints: 8389 Sorted by residual: bond pdb=" CA ARG L 7 " pdb=" C ARG L 7 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.24e-02 6.50e+03 1.40e+01 bond pdb=" C HIS L 5 " pdb=" O HIS L 5 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.17e-02 7.31e+03 1.08e+01 bond pdb=" N ARG L 7 " pdb=" CA ARG L 7 " ideal model delta sigma weight residual 1.455 1.419 0.036 1.32e-02 5.74e+03 7.51e+00 bond pdb=" CA HIS L 5 " pdb=" CB HIS L 5 " ideal model delta sigma weight residual 1.527 1.493 0.034 1.44e-02 4.82e+03 5.45e+00 bond pdb=" C HIS L 5 " pdb=" N PHE L 6 " ideal model delta sigma weight residual 1.327 1.303 0.024 1.06e-02 8.90e+03 5.04e+00 ... (remaining 8384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 11138 2.17 - 4.34: 190 4.34 - 6.51: 25 6.51 - 8.67: 5 8.67 - 10.84: 2 Bond angle restraints: 11360 Sorted by residual: angle pdb=" C PHE L 6 " pdb=" CA PHE L 6 " pdb=" CB PHE L 6 " ideal model delta sigma weight residual 116.34 110.74 5.60 1.40e+00 5.10e-01 1.60e+01 angle pdb=" N ARG L 7 " pdb=" CA ARG L 7 " pdb=" C ARG L 7 " ideal model delta sigma weight residual 108.74 113.59 -4.85 1.38e+00 5.25e-01 1.23e+01 angle pdb=" N ASN G 24 " pdb=" CA ASN G 24 " pdb=" C ASN G 24 " ideal model delta sigma weight residual 114.56 110.57 3.99 1.27e+00 6.20e-01 9.85e+00 angle pdb=" C LYS N 33 " pdb=" N MET N 34 " pdb=" CA MET N 34 " ideal model delta sigma weight residual 122.59 118.15 4.44 1.57e+00 4.06e-01 8.00e+00 angle pdb=" CB MET R 97 " pdb=" CG MET R 97 " pdb=" SD MET R 97 " ideal model delta sigma weight residual 112.70 104.34 8.36 3.00e+00 1.11e-01 7.77e+00 ... (remaining 11355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 4498 17.49 - 34.97: 413 34.97 - 52.46: 79 52.46 - 69.94: 12 69.94 - 87.42: 8 Dihedral angle restraints: 5010 sinusoidal: 1972 harmonic: 3038 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.72 34.28 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA ASP G 36 " pdb=" C ASP G 36 " pdb=" N LEU G 37 " pdb=" CA LEU G 37 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR R 182 " pdb=" C TYR R 182 " pdb=" N SER R 183 " pdb=" CA SER R 183 " ideal model delta harmonic sigma weight residual 180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 5007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 754 0.037 - 0.074: 378 0.074 - 0.111: 116 0.111 - 0.148: 38 0.148 - 0.185: 5 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CA HIS L 5 " pdb=" N HIS L 5 " pdb=" C HIS L 5 " pdb=" CB HIS L 5 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA VAL L 2 " pdb=" N VAL L 2 " pdb=" C VAL L 2 " pdb=" CB VAL L 2 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 1288 not shown) Planarity restraints: 1444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " 0.019 2.00e-02 2.50e+03 1.37e-02 4.69e+00 pdb=" CG TRP A 281 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 256 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO R 257 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 257 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 257 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO N 14 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.026 5.00e-02 4.00e+02 ... (remaining 1441 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 907 2.74 - 3.28: 7965 3.28 - 3.82: 13555 3.82 - 4.36: 16080 4.36 - 4.90: 28045 Nonbonded interactions: 66552 Sorted by model distance: nonbonded pdb=" NE1 TRP R 255 " pdb=" OD1 ASN R 291 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG A 232 " pdb=" OD2 ASP N 109 " model vdw 2.227 3.120 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.228 3.120 nonbonded pdb=" OE2 GLU R 94 " pdb="CA CA R 501 " model vdw 2.243 2.510 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.244 3.040 ... (remaining 66547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.590 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 : 0.007 0.056 8389 Z= 0.486 Angle : 0.728 10.843 11360 Z= 0.406 Chirality : 0.049 0.185 1291 Planarity : 0.005 0.049 1444 Dihedral : 14.043 87.425 3030 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.11 % Allowed : 0.55 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.25), residues: 1025 helix: 0.31 (0.26), residues: 401 sheet: -0.75 (0.32), residues: 234 loop : -1.50 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 281 HIS 0.008 0.002 HIS L 5 PHE 0.030 0.002 PHE B 235 TYR 0.027 0.002 TYR B 59 ARG 0.009 0.001 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 240 average time/residue: 1.2741 time to fit residues: 324.3650 Evaluate side-chains 157 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 75 GLN B 91 HIS B 155 ASN B 259 GLN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN G 44 HIS L 5 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.125671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.088184 restraints weight = 15825.648| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.91 r_work: 0.3112 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8389 Z= 0.264 Angle : 0.673 13.356 11360 Z= 0.344 Chirality : 0.043 0.136 1291 Planarity : 0.004 0.049 1444 Dihedral : 5.003 47.759 1137 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.00 % Allowed : 13.65 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1025 helix: 1.01 (0.26), residues: 398 sheet: -0.33 (0.34), residues: 219 loop : -1.22 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.002 PHE R 259 TYR 0.017 0.002 TYR R 277 ARG 0.008 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.802 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 229 ASP cc_start: 0.8428 (t0) cc_final: 0.7811 (t0) REVERT: A 279 ASN cc_start: 0.9127 (t0) cc_final: 0.8876 (t0) REVERT: B 172 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8924 (tp30) REVERT: B 175 GLN cc_start: 0.8792 (mp10) cc_final: 0.8566 (mp10) REVERT: B 260 GLU cc_start: 0.8634 (pp20) cc_final: 0.8353 (tm-30) REVERT: B 280 LYS cc_start: 0.9019 (tptp) cc_final: 0.8557 (tptp) REVERT: B 292 PHE cc_start: 0.8992 (m-10) cc_final: 0.8771 (m-10) REVERT: B 325 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8922 (mpp) REVERT: R 41 LYS cc_start: 0.8719 (ttpt) cc_final: 0.8281 (tmmt) REVERT: R 277 TYR cc_start: 0.8784 (t80) cc_final: 0.8403 (t80) REVERT: R 281 PHE cc_start: 0.8296 (t80) cc_final: 0.8086 (t80) REVERT: G 21 MET cc_start: 0.8042 (tpt) cc_final: 0.7705 (tpt) REVERT: G 24 ASN cc_start: 0.9185 (t0) cc_final: 0.8507 (m110) REVERT: G 28 ILE cc_start: 0.8814 (mp) cc_final: 0.8588 (mp) REVERT: G 47 GLU cc_start: 0.8105 (pm20) cc_final: 0.7717 (pm20) outliers start: 27 outliers final: 12 residues processed: 178 average time/residue: 1.3075 time to fit residues: 247.0074 Evaluate side-chains 154 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain G residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 95 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 291 ASN L 5 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.127693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.091397 restraints weight = 16199.752| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.96 r_work: 0.3140 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 0.065 8389 Z= 0.192 Angle : 0.629 13.358 11360 Z= 0.317 Chirality : 0.041 0.144 1291 Planarity : 0.004 0.043 1444 Dihedral : 4.712 47.751 1135 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.11 % Allowed : 15.32 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1025 helix: 1.54 (0.27), residues: 394 sheet: -0.27 (0.33), residues: 239 loop : -1.08 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.008 0.001 HIS R 261 PHE 0.012 0.001 PHE R 310 TYR 0.013 0.001 TYR N 60 ARG 0.008 0.001 ARG L 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8305 (tt0) cc_final: 0.7917 (tm-30) REVERT: A 229 ASP cc_start: 0.8435 (t0) cc_final: 0.7809 (t0) REVERT: A 279 ASN cc_start: 0.9108 (t0) cc_final: 0.8860 (t0) REVERT: A 302 LEU cc_start: 0.9732 (mm) cc_final: 0.9462 (mm) REVERT: A 349 SER cc_start: 0.9282 (OUTLIER) cc_final: 0.8864 (p) REVERT: B 172 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8994 (tp30) REVERT: B 175 GLN cc_start: 0.8796 (mp10) cc_final: 0.8521 (mp10) REVERT: B 227 SER cc_start: 0.8975 (t) cc_final: 0.8740 (p) REVERT: B 280 LYS cc_start: 0.8927 (tptp) cc_final: 0.8265 (tptp) REVERT: B 292 PHE cc_start: 0.9094 (m-10) cc_final: 0.8833 (m-10) REVERT: R 41 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8147 (tmmt) REVERT: R 65 ARG cc_start: 0.8621 (ttp-170) cc_final: 0.8123 (ttm170) REVERT: R 111 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8233 (tp-100) REVERT: R 115 HIS cc_start: 0.7797 (m90) cc_final: 0.7235 (m90) REVERT: R 116 MET cc_start: 0.8603 (tmm) cc_final: 0.8041 (mpt) REVERT: R 277 TYR cc_start: 0.8834 (t80) cc_final: 0.8376 (t80) REVERT: R 305 GLU cc_start: 0.8477 (pm20) cc_final: 0.8108 (pm20) REVERT: G 17 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8488 (pt0) REVERT: G 21 MET cc_start: 0.8187 (tpt) cc_final: 0.7769 (tpt) REVERT: G 24 ASN cc_start: 0.9238 (t0) cc_final: 0.8615 (m110) REVERT: G 28 ILE cc_start: 0.8820 (mp) cc_final: 0.8572 (mp) REVERT: G 29 LYS cc_start: 0.9311 (mmmt) cc_final: 0.9018 (mmmt) REVERT: L 1 TYR cc_start: 0.7230 (t80) cc_final: 0.6878 (t80) outliers start: 28 outliers final: 8 residues processed: 177 average time/residue: 1.2834 time to fit residues: 240.5777 Evaluate side-chains 156 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 59 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN R 291 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.125991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.089249 restraints weight = 16066.223| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.90 r_work: 0.3109 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8389 Z= 0.252 Angle : 0.641 13.661 11360 Z= 0.322 Chirality : 0.042 0.135 1291 Planarity : 0.004 0.043 1444 Dihedral : 4.671 49.019 1135 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.88 % Allowed : 17.20 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.27), residues: 1025 helix: 1.60 (0.27), residues: 399 sheet: -0.22 (0.34), residues: 240 loop : -1.03 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 64 PHE 0.012 0.001 PHE R 259 TYR 0.010 0.001 TYR L 1 ARG 0.008 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8497 (t0) cc_final: 0.7883 (t0) REVERT: A 253 TYR cc_start: 0.8841 (m-80) cc_final: 0.8435 (m-80) REVERT: A 279 ASN cc_start: 0.9155 (t0) cc_final: 0.8915 (t0) REVERT: A 349 SER cc_start: 0.9340 (OUTLIER) cc_final: 0.8908 (p) REVERT: B 32 GLN cc_start: 0.8874 (mt0) cc_final: 0.8637 (mt0) REVERT: B 172 GLU cc_start: 0.9262 (mm-30) cc_final: 0.9045 (tp30) REVERT: B 227 SER cc_start: 0.8940 (t) cc_final: 0.8707 (p) REVERT: B 280 LYS cc_start: 0.8992 (tptp) cc_final: 0.8277 (tptp) REVERT: B 291 ASP cc_start: 0.8937 (m-30) cc_final: 0.8590 (m-30) REVERT: B 292 PHE cc_start: 0.9189 (m-10) cc_final: 0.8938 (m-10) REVERT: R 41 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8159 (tmmt) REVERT: R 65 ARG cc_start: 0.8476 (tpp-160) cc_final: 0.8050 (ttm170) REVERT: R 85 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8601 (ppp) REVERT: R 191 CYS cc_start: 0.8490 (t) cc_final: 0.8125 (t) REVERT: R 277 TYR cc_start: 0.8870 (t80) cc_final: 0.8439 (t80) REVERT: R 281 PHE cc_start: 0.8370 (t80) cc_final: 0.8094 (t80) REVERT: R 305 GLU cc_start: 0.8398 (pm20) cc_final: 0.7992 (pm20) REVERT: R 307 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8478 (mmm-85) REVERT: R 308 ASN cc_start: 0.8730 (m-40) cc_final: 0.8194 (p0) REVERT: G 17 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8549 (pt0) REVERT: G 21 MET cc_start: 0.8358 (tpt) cc_final: 0.7816 (tpt) REVERT: G 24 ASN cc_start: 0.9228 (t0) cc_final: 0.8750 (m110) REVERT: G 28 ILE cc_start: 0.8899 (mp) cc_final: 0.8668 (mp) REVERT: L 1 TYR cc_start: 0.7371 (t80) cc_final: 0.7002 (t80) outliers start: 35 outliers final: 15 residues processed: 174 average time/residue: 1.2497 time to fit residues: 230.6710 Evaluate side-chains 162 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 0.4980 chunk 57 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 230 ASN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.126108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.089110 restraints weight = 15770.742| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.88 r_work: 0.3129 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8389 Z= 0.188 Angle : 0.638 13.676 11360 Z= 0.318 Chirality : 0.041 0.136 1291 Planarity : 0.003 0.041 1444 Dihedral : 4.556 48.296 1135 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.77 % Allowed : 20.09 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 1025 helix: 1.75 (0.27), residues: 398 sheet: -0.13 (0.33), residues: 246 loop : -0.96 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS R 261 PHE 0.025 0.001 PHE R 120 TYR 0.014 0.001 TYR N 60 ARG 0.008 0.001 ARG L 7 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8471 (t0) cc_final: 0.7816 (t0) REVERT: A 253 TYR cc_start: 0.8804 (m-80) cc_final: 0.8457 (m-80) REVERT: A 279 ASN cc_start: 0.9166 (t0) cc_final: 0.8920 (t0) REVERT: A 349 SER cc_start: 0.9330 (OUTLIER) cc_final: 0.8880 (p) REVERT: B 32 GLN cc_start: 0.8888 (mt0) cc_final: 0.8669 (mt0) REVERT: B 59 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8427 (m-80) REVERT: B 172 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8830 (tp30) REVERT: B 175 GLN cc_start: 0.8706 (mp10) cc_final: 0.8471 (mp10) REVERT: B 217 MET cc_start: 0.8729 (pmt) cc_final: 0.8204 (pmm) REVERT: B 260 GLU cc_start: 0.8520 (pp20) cc_final: 0.8238 (tm-30) REVERT: B 280 LYS cc_start: 0.8994 (tptp) cc_final: 0.8092 (tptp) REVERT: B 291 ASP cc_start: 0.8913 (m-30) cc_final: 0.8506 (m-30) REVERT: B 292 PHE cc_start: 0.9197 (m-10) cc_final: 0.8918 (m-10) REVERT: R 41 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8112 (tmmt) REVERT: R 65 ARG cc_start: 0.8488 (tpp-160) cc_final: 0.8029 (ttm170) REVERT: R 85 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8672 (ppp) REVERT: R 191 CYS cc_start: 0.8487 (t) cc_final: 0.8147 (t) REVERT: R 253 PHE cc_start: 0.8809 (m-10) cc_final: 0.8038 (t80) REVERT: R 277 TYR cc_start: 0.8861 (t80) cc_final: 0.8437 (t80) REVERT: R 281 PHE cc_start: 0.8254 (t80) cc_final: 0.8005 (t80) REVERT: R 305 GLU cc_start: 0.8415 (pm20) cc_final: 0.8140 (pm20) REVERT: R 307 ARG cc_start: 0.8723 (mmm-85) cc_final: 0.8389 (mmm-85) REVERT: R 308 ASN cc_start: 0.8740 (m-40) cc_final: 0.8239 (p0) REVERT: G 17 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8570 (pt0) REVERT: G 21 MET cc_start: 0.8472 (tpt) cc_final: 0.7955 (tpt) REVERT: G 24 ASN cc_start: 0.9162 (t0) cc_final: 0.8713 (m110) REVERT: G 28 ILE cc_start: 0.8897 (mp) cc_final: 0.8652 (mp) REVERT: G 47 GLU cc_start: 0.8175 (pm20) cc_final: 0.7662 (pm20) REVERT: L 1 TYR cc_start: 0.7431 (t80) cc_final: 0.7047 (t80) REVERT: N 47 TRP cc_start: 0.8038 (t60) cc_final: 0.7769 (t60) outliers start: 25 outliers final: 11 residues processed: 171 average time/residue: 1.2612 time to fit residues: 230.0133 Evaluate side-chains 156 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain G residue 51 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 44 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 chunk 68 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 59 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 HIS N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.124526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087145 restraints weight = 15807.176| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.86 r_work: 0.3102 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8389 Z= 0.242 Angle : 0.651 12.836 11360 Z= 0.324 Chirality : 0.042 0.143 1291 Planarity : 0.003 0.044 1444 Dihedral : 4.548 48.590 1135 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.66 % Allowed : 19.64 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1025 helix: 1.70 (0.26), residues: 403 sheet: -0.11 (0.33), residues: 237 loop : -0.88 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.002 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.010 0.001 TYR R 207 ARG 0.007 0.001 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9309 (pptt) cc_final: 0.9056 (pptt) REVERT: A 229 ASP cc_start: 0.8557 (t0) cc_final: 0.7931 (t0) REVERT: A 253 TYR cc_start: 0.8884 (m-80) cc_final: 0.8451 (m-80) REVERT: A 268 GLU cc_start: 0.8688 (mp0) cc_final: 0.8450 (tp30) REVERT: A 279 ASN cc_start: 0.9190 (t0) cc_final: 0.8943 (t0) REVERT: B 172 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8980 (tp30) REVERT: B 175 GLN cc_start: 0.8734 (mp10) cc_final: 0.8514 (mp10) REVERT: B 226 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7845 (mm-30) REVERT: B 234 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.8059 (m-80) REVERT: B 280 LYS cc_start: 0.8994 (tptp) cc_final: 0.8196 (tptp) REVERT: B 291 ASP cc_start: 0.8939 (m-30) cc_final: 0.8564 (m-30) REVERT: B 292 PHE cc_start: 0.9213 (m-10) cc_final: 0.8968 (m-10) REVERT: R 41 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8050 (tmmt) REVERT: R 82 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8419 (p) REVERT: R 85 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8621 (ppp) REVERT: R 156 MET cc_start: 0.8568 (tpp) cc_final: 0.8284 (tpp) REVERT: R 191 CYS cc_start: 0.8582 (t) cc_final: 0.8228 (t) REVERT: R 253 PHE cc_start: 0.8845 (m-10) cc_final: 0.8094 (t80) REVERT: R 277 TYR cc_start: 0.8880 (t80) cc_final: 0.8522 (t80) REVERT: R 281 PHE cc_start: 0.8358 (t80) cc_final: 0.8096 (t80) REVERT: R 307 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.8464 (mmm-85) REVERT: R 308 ASN cc_start: 0.8707 (m-40) cc_final: 0.8228 (p0) REVERT: G 17 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8620 (pt0) REVERT: G 21 MET cc_start: 0.8623 (tpt) cc_final: 0.8105 (tpt) REVERT: G 24 ASN cc_start: 0.9166 (t0) cc_final: 0.8731 (m110) REVERT: G 28 ILE cc_start: 0.8939 (mp) cc_final: 0.8736 (mp) REVERT: G 47 GLU cc_start: 0.8176 (pm20) cc_final: 0.7752 (pm20) REVERT: L 7 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8047 (ttm-80) REVERT: N 47 TRP cc_start: 0.8339 (t60) cc_final: 0.8053 (t60) REVERT: N 83 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7547 (mmp) outliers start: 33 outliers final: 13 residues processed: 168 average time/residue: 1.2297 time to fit residues: 219.6827 Evaluate side-chains 160 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.126104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.088637 restraints weight = 15975.612| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.91 r_work: 0.3124 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8389 Z= 0.202 Angle : 0.654 14.134 11360 Z= 0.325 Chirality : 0.041 0.134 1291 Planarity : 0.003 0.042 1444 Dihedral : 4.494 47.990 1135 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.11 % Allowed : 20.20 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.27), residues: 1025 helix: 1.87 (0.26), residues: 397 sheet: -0.09 (0.33), residues: 245 loop : -0.81 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS R 261 PHE 0.011 0.001 PHE B 199 TYR 0.018 0.001 TYR L 1 ARG 0.008 0.001 ARG R 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9294 (pptt) cc_final: 0.9032 (pptt) REVERT: A 229 ASP cc_start: 0.8565 (t0) cc_final: 0.7915 (t0) REVERT: A 253 TYR cc_start: 0.8800 (m-80) cc_final: 0.8372 (m-80) REVERT: A 268 GLU cc_start: 0.8659 (mp0) cc_final: 0.8424 (tp30) REVERT: A 279 ASN cc_start: 0.9179 (t0) cc_final: 0.8941 (t0) REVERT: B 172 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8968 (tp30) REVERT: B 175 GLN cc_start: 0.8746 (mp10) cc_final: 0.8506 (mp10) REVERT: B 217 MET cc_start: 0.8776 (pmt) cc_final: 0.8284 (pmm) REVERT: B 226 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 234 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: B 280 LYS cc_start: 0.8971 (tptp) cc_final: 0.8000 (tptp) REVERT: B 291 ASP cc_start: 0.8924 (m-30) cc_final: 0.8539 (m-30) REVERT: B 292 PHE cc_start: 0.9215 (m-10) cc_final: 0.8943 (m-10) REVERT: R 41 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8177 (tmmt) REVERT: R 82 VAL cc_start: 0.8641 (p) cc_final: 0.8439 (p) REVERT: R 84 ASP cc_start: 0.8947 (m-30) cc_final: 0.8732 (t0) REVERT: R 85 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8566 (ppp) REVERT: R 156 MET cc_start: 0.8507 (tpp) cc_final: 0.8179 (tpp) REVERT: R 191 CYS cc_start: 0.8518 (t) cc_final: 0.8172 (t) REVERT: R 253 PHE cc_start: 0.8780 (m-10) cc_final: 0.8074 (t80) REVERT: R 277 TYR cc_start: 0.8865 (t80) cc_final: 0.8470 (t80) REVERT: R 281 PHE cc_start: 0.8255 (t80) cc_final: 0.8004 (t80) REVERT: R 291 ASN cc_start: 0.8056 (t0) cc_final: 0.7636 (t0) REVERT: R 305 GLU cc_start: 0.8471 (pm20) cc_final: 0.7753 (pm20) REVERT: R 307 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8476 (mmm-85) REVERT: R 308 ASN cc_start: 0.8718 (m-40) cc_final: 0.8254 (p0) REVERT: G 21 MET cc_start: 0.8637 (tpt) cc_final: 0.8431 (tpt) REVERT: G 28 ILE cc_start: 0.8946 (mp) cc_final: 0.8721 (mp) REVERT: G 47 GLU cc_start: 0.8236 (pm20) cc_final: 0.7860 (pm20) REVERT: L 7 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8142 (ttm-80) REVERT: N 47 TRP cc_start: 0.8429 (t60) cc_final: 0.8226 (t60) REVERT: N 83 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7481 (mmt) REVERT: N 117 TYR cc_start: 0.8002 (m-80) cc_final: 0.7734 (m-10) outliers start: 28 outliers final: 13 residues processed: 166 average time/residue: 1.2338 time to fit residues: 217.3905 Evaluate side-chains 157 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.0020 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 75 GLN R 70 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.126515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088969 restraints weight = 16083.074| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.88 r_work: 0.3129 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8389 Z= 0.204 Angle : 0.670 13.479 11360 Z= 0.334 Chirality : 0.042 0.174 1291 Planarity : 0.004 0.043 1444 Dihedral : 4.503 48.047 1135 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.44 % Allowed : 20.75 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.27), residues: 1025 helix: 1.90 (0.26), residues: 397 sheet: 0.09 (0.34), residues: 233 loop : -0.80 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS R 261 PHE 0.011 0.001 PHE B 199 TYR 0.019 0.001 TYR L 1 ARG 0.009 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9295 (pptt) cc_final: 0.9022 (pptt) REVERT: A 229 ASP cc_start: 0.8497 (t0) cc_final: 0.7839 (t0) REVERT: A 253 TYR cc_start: 0.8806 (m-80) cc_final: 0.8409 (m-80) REVERT: A 268 GLU cc_start: 0.8676 (mp0) cc_final: 0.8455 (tp30) REVERT: A 279 ASN cc_start: 0.9221 (t0) cc_final: 0.8954 (t0) REVERT: B 172 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8995 (tp30) REVERT: B 175 GLN cc_start: 0.8746 (mp10) cc_final: 0.8523 (mp10) REVERT: B 217 MET cc_start: 0.8733 (pmt) cc_final: 0.8204 (pmm) REVERT: B 234 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: B 280 LYS cc_start: 0.8951 (tptp) cc_final: 0.8225 (tptp) REVERT: B 291 ASP cc_start: 0.8932 (m-30) cc_final: 0.8535 (m-30) REVERT: B 292 PHE cc_start: 0.9291 (m-10) cc_final: 0.9030 (m-10) REVERT: R 41 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8304 (tmmt) REVERT: R 73 MET cc_start: 0.8975 (ptm) cc_final: 0.8234 (ppp) REVERT: R 82 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8421 (p) REVERT: R 85 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8574 (ppp) REVERT: R 156 MET cc_start: 0.8552 (tpp) cc_final: 0.8240 (tpp) REVERT: R 191 CYS cc_start: 0.8545 (t) cc_final: 0.8219 (t) REVERT: R 253 PHE cc_start: 0.8818 (m-10) cc_final: 0.8095 (t80) REVERT: R 277 TYR cc_start: 0.8890 (t80) cc_final: 0.8422 (t80) REVERT: R 281 PHE cc_start: 0.8246 (t80) cc_final: 0.8021 (t80) REVERT: R 291 ASN cc_start: 0.8151 (t0) cc_final: 0.7791 (t0) REVERT: R 302 ARG cc_start: 0.8924 (mmm-85) cc_final: 0.8692 (mmm-85) REVERT: R 305 GLU cc_start: 0.8521 (pm20) cc_final: 0.8047 (pm20) REVERT: R 307 ARG cc_start: 0.8724 (mmm-85) cc_final: 0.8485 (mmm-85) REVERT: R 308 ASN cc_start: 0.8718 (m-40) cc_final: 0.8282 (p0) REVERT: G 21 MET cc_start: 0.8629 (tpt) cc_final: 0.8384 (tpt) REVERT: G 28 ILE cc_start: 0.8918 (mp) cc_final: 0.8683 (mp) REVERT: G 47 GLU cc_start: 0.8279 (pm20) cc_final: 0.7924 (pm20) REVERT: N 83 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7491 (mmt) REVERT: N 117 TYR cc_start: 0.8091 (m-80) cc_final: 0.7750 (m-10) outliers start: 22 outliers final: 14 residues processed: 159 average time/residue: 1.2766 time to fit residues: 214.9802 Evaluate side-chains 161 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN N 35 ASN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.125461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.087972 restraints weight = 16281.844| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.90 r_work: 0.3121 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8389 Z= 0.225 Angle : 0.688 13.301 11360 Z= 0.341 Chirality : 0.042 0.151 1291 Planarity : 0.004 0.066 1444 Dihedral : 4.502 48.187 1135 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.77 % Allowed : 20.98 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.27), residues: 1025 helix: 1.82 (0.26), residues: 399 sheet: -0.03 (0.33), residues: 245 loop : -0.74 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.002 0.001 HIS R 261 PHE 0.012 0.001 PHE R 310 TYR 0.018 0.001 TYR L 1 ARG 0.016 0.001 ARG L 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8551 (t0) cc_final: 0.7889 (t0) REVERT: A 253 TYR cc_start: 0.8811 (m-80) cc_final: 0.8424 (m-80) REVERT: A 268 GLU cc_start: 0.8677 (mp0) cc_final: 0.8457 (tp30) REVERT: A 279 ASN cc_start: 0.9227 (t0) cc_final: 0.8962 (t0) REVERT: B 172 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8883 (tp30) REVERT: B 175 GLN cc_start: 0.8770 (mp10) cc_final: 0.8527 (mp10) REVERT: B 217 MET cc_start: 0.8744 (pmt) cc_final: 0.8240 (pmm) REVERT: B 234 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: B 280 LYS cc_start: 0.8954 (tptp) cc_final: 0.8250 (tptp) REVERT: B 291 ASP cc_start: 0.8921 (m-30) cc_final: 0.8524 (m-30) REVERT: B 292 PHE cc_start: 0.9277 (m-10) cc_final: 0.9007 (m-10) REVERT: R 41 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8356 (tmmt) REVERT: R 73 MET cc_start: 0.8961 (ptm) cc_final: 0.8238 (ppp) REVERT: R 85 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8569 (ppp) REVERT: R 156 MET cc_start: 0.8557 (tpp) cc_final: 0.8257 (tpp) REVERT: R 191 CYS cc_start: 0.8564 (t) cc_final: 0.8074 (t) REVERT: R 253 PHE cc_start: 0.8839 (m-10) cc_final: 0.8101 (t80) REVERT: R 277 TYR cc_start: 0.8899 (t80) cc_final: 0.8501 (t80) REVERT: R 281 PHE cc_start: 0.8352 (t80) cc_final: 0.8105 (t80) REVERT: R 302 ARG cc_start: 0.8954 (mmm-85) cc_final: 0.8706 (mmm-85) REVERT: R 307 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8498 (mmm-85) REVERT: G 21 MET cc_start: 0.8629 (tpt) cc_final: 0.8412 (tpt) REVERT: G 47 GLU cc_start: 0.8445 (pm20) cc_final: 0.7996 (pm20) REVERT: N 83 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7629 (mmt) REVERT: N 117 TYR cc_start: 0.8118 (m-80) cc_final: 0.7792 (m-10) outliers start: 25 outliers final: 17 residues processed: 163 average time/residue: 1.2418 time to fit residues: 214.6713 Evaluate side-chains 160 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 97 optimal weight: 0.0870 chunk 24 optimal weight: 6.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.126079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.088668 restraints weight = 16006.896| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.89 r_work: 0.3135 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8389 Z= 0.221 Angle : 0.738 13.146 11360 Z= 0.365 Chirality : 0.042 0.160 1291 Planarity : 0.004 0.049 1444 Dihedral : 4.485 48.014 1135 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.55 % Allowed : 22.64 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.27), residues: 1025 helix: 1.75 (0.27), residues: 397 sheet: -0.07 (0.32), residues: 251 loop : -0.74 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS R 261 PHE 0.011 0.001 PHE B 199 TYR 0.020 0.001 TYR L 1 ARG 0.014 0.001 ARG L 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8579 (t0) cc_final: 0.7987 (t0) REVERT: A 253 TYR cc_start: 0.8825 (m-80) cc_final: 0.8372 (m-80) REVERT: A 268 GLU cc_start: 0.8662 (mp0) cc_final: 0.8450 (tp30) REVERT: A 279 ASN cc_start: 0.9208 (t0) cc_final: 0.8985 (t0) REVERT: B 172 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8979 (tp30) REVERT: B 175 GLN cc_start: 0.8759 (mp10) cc_final: 0.8530 (mp10) REVERT: B 217 MET cc_start: 0.8763 (pmt) cc_final: 0.8237 (pmm) REVERT: B 226 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8044 (tp30) REVERT: B 234 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7937 (m-80) REVERT: B 280 LYS cc_start: 0.8945 (tptp) cc_final: 0.8305 (tptp) REVERT: B 291 ASP cc_start: 0.8945 (m-30) cc_final: 0.8521 (m-30) REVERT: B 292 PHE cc_start: 0.9277 (m-10) cc_final: 0.9011 (m-10) REVERT: R 41 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8402 (tmmt) REVERT: R 73 MET cc_start: 0.8960 (ptm) cc_final: 0.8331 (ppp) REVERT: R 97 MET cc_start: 0.8593 (ttt) cc_final: 0.8218 (tmm) REVERT: R 156 MET cc_start: 0.8552 (tpp) cc_final: 0.8267 (tpp) REVERT: R 171 CYS cc_start: 0.8895 (m) cc_final: 0.8571 (m) REVERT: R 253 PHE cc_start: 0.8842 (m-10) cc_final: 0.8072 (t80) REVERT: R 277 TYR cc_start: 0.8901 (t80) cc_final: 0.8410 (t80) REVERT: R 281 PHE cc_start: 0.8280 (t80) cc_final: 0.8041 (t80) REVERT: R 291 ASN cc_start: 0.8056 (t0) cc_final: 0.7711 (t0) REVERT: R 307 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8491 (mmm-85) REVERT: G 47 GLU cc_start: 0.8437 (pm20) cc_final: 0.8028 (pm20) REVERT: N 83 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7638 (mmt) REVERT: N 117 TYR cc_start: 0.8054 (m-80) cc_final: 0.7743 (m-10) outliers start: 23 outliers final: 17 residues processed: 162 average time/residue: 1.2875 time to fit residues: 220.9383 Evaluate side-chains 158 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.126565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089030 restraints weight = 16164.804| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.89 r_work: 0.3141 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8389 Z= 0.231 Angle : 0.769 13.059 11360 Z= 0.378 Chirality : 0.043 0.210 1291 Planarity : 0.004 0.060 1444 Dihedral : 4.518 48.396 1135 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.44 % Allowed : 22.97 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 1025 helix: 1.78 (0.27), residues: 390 sheet: -0.01 (0.33), residues: 234 loop : -0.69 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.003 0.001 HIS G 44 PHE 0.011 0.001 PHE B 199 TYR 0.021 0.001 TYR L 1 ARG 0.016 0.001 ARG L 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6993.75 seconds wall clock time: 123 minutes 56.44 seconds (7436.44 seconds total)