Starting phenix.real_space_refine on Fri Nov 15 03:41:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioc_35615/11_2024/8ioc_35615.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioc_35615/11_2024/8ioc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioc_35615/11_2024/8ioc_35615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioc_35615/11_2024/8ioc_35615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioc_35615/11_2024/8ioc_35615.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ioc_35615/11_2024/8ioc_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-5513/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: 5.10, per 1000 atoms: 0.62 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: 1.86 Conformation dependent library (CDL) restraints added in 1.2 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: 0.85 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: 2.39 Time building geometry restraints manager: 2.20 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: 0.740 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.610 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.660 ------------------------------------------------------------------------------- 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 : 0.966 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: 1.2430 time to fit residues: 315.9569 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 : 0.861 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.940 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 279 ASN cc_start: 0.8884 (t0) cc_final: 0.8653 (t0) REVERT: G 28 ILE cc_start: 0.8156 (mp) cc_final: 0.7882 (mp) outliers start: 27 outliers final: 12 residues processed: 178 average time/residue: 1.3666 time to fit residues: 257.5222 Evaluate side-chains 146 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 75 GLN R 291 ASN N 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 8389 Z= 0.323 Angle : 0.680 13.604 11360 Z= 0.345 Chirality : 0.043 0.134 1291 Planarity : 0.004 0.046 1444 Dihedral : 4.942 51.317 1135 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.22 % Allowed : 14.76 % Favored : 81.02 % 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: -0.02 (0.26), residues: 1025 helix: 1.33 (0.26), residues: 394 sheet: -0.36 (0.33), residues: 238 loop : -1.12 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.005 0.001 HIS R 261 PHE 0.013 0.002 PHE B 151 TYR 0.023 0.002 TYR R 277 ARG 0.009 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 190 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 115 HIS cc_start: 0.6519 (m90) cc_final: 0.6242 (m90) REVERT: G 14 LYS cc_start: 0.8820 (mmtm) cc_final: 0.8600 (mmtm) REVERT: G 21 MET cc_start: 0.7023 (tpt) cc_final: 0.6714 (tpp) REVERT: G 28 ILE cc_start: 0.8223 (mp) cc_final: 0.7971 (mp) REVERT: N 34 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6445 (mtt) outliers start: 38 outliers final: 17 residues processed: 174 average time/residue: 1.2607 time to fit residues: 232.7129 Evaluate side-chains 155 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 51 LEU Chi-restraints excluded: chain B residue 59 TYR 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 59 VAL 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 Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 34 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.0970 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 HIS N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8389 Z= 0.393 Angle : 0.711 13.924 11360 Z= 0.363 Chirality : 0.045 0.169 1291 Planarity : 0.004 0.049 1444 Dihedral : 5.080 55.261 1135 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.44 % Allowed : 17.98 % Favored : 77.58 % 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: -0.12 (0.26), residues: 1025 helix: 1.16 (0.26), residues: 407 sheet: -0.39 (0.33), residues: 236 loop : -1.16 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.004 0.001 HIS B 62 PHE 0.017 0.002 PHE B 151 TYR 0.023 0.002 TYR R 277 ARG 0.012 0.001 ARG L 7 *********************** 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 185 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.8957 (t0) cc_final: 0.8756 (t0) REVERT: R 65 ARG cc_start: 0.7568 (ttm170) cc_final: 0.7263 (ttp80) REVERT: G 28 ILE cc_start: 0.8223 (mp) cc_final: 0.8000 (mp) REVERT: N 117 TYR cc_start: 0.7946 (m-80) cc_final: 0.7727 (m-10) outliers start: 40 outliers final: 21 residues processed: 165 average time/residue: 1.2339 time to fit residues: 216.4879 Evaluate side-chains 151 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 290 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain G residue 51 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 1 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 0.0010 chunk 84 optimal weight: 6.9990 chunk 68 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.5946 ------------------------------------------------------------------------------- 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 B 230 ASN R 111 GLN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4008 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= 0.183 Angle : 0.658 13.677 11360 Z= 0.327 Chirality : 0.042 0.159 1291 Planarity : 0.004 0.081 1444 Dihedral : 4.729 49.245 1135 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.00 % Allowed : 18.76 % Favored : 77.25 % 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: 0.26 (0.26), residues: 1025 helix: 1.52 (0.26), residues: 405 sheet: -0.12 (0.34), residues: 230 loop : -1.05 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.003 0.001 HIS R 261 PHE 0.013 0.001 PHE R 310 TYR 0.022 0.001 TYR R 277 ARG 0.015 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 193 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 280 LYS cc_start: 0.7763 (tptp) cc_final: 0.7440 (tptp) REVERT: G 28 ILE cc_start: 0.8211 (mp) cc_final: 0.8008 (mp) outliers start: 36 outliers final: 15 residues processed: 175 average time/residue: 1.2020 time to fit residues: 223.7238 Evaluate side-chains 151 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 53 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 306 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 57 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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** B 75 GLN R 111 GLN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8389 Z= 0.411 Angle : 0.752 12.976 11360 Z= 0.379 Chirality : 0.044 0.134 1291 Planarity : 0.004 0.046 1444 Dihedral : 4.972 53.011 1135 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.11 % Allowed : 20.98 % Favored : 74.92 % 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: 0.03 (0.26), residues: 1025 helix: 1.36 (0.26), residues: 406 sheet: -0.41 (0.33), residues: 240 loop : -1.10 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 47 HIS 0.008 0.001 HIS R 115 PHE 0.019 0.002 PHE B 199 TYR 0.018 0.002 TYR R 277 ARG 0.016 0.001 ARG R 65 *********************** 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 179 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: R 307 ARG cc_start: 0.8282 (mmm-85) cc_final: 0.7776 (mmm-85) REVERT: G 28 ILE cc_start: 0.8344 (mp) cc_final: 0.7713 (mp) outliers start: 37 outliers final: 20 residues processed: 160 average time/residue: 1.2881 time to fit residues: 218.8801 Evaluate side-chains 150 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 61 LEU 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 217 HIS Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 290 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8389 Z= 0.223 Angle : 0.706 12.449 11360 Z= 0.355 Chirality : 0.043 0.142 1291 Planarity : 0.004 0.043 1444 Dihedral : 4.797 51.005 1135 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.11 % Allowed : 22.42 % Favored : 74.47 % 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: 0.22 (0.26), residues: 1025 helix: 1.51 (0.26), residues: 407 sheet: -0.26 (0.33), residues: 240 loop : -1.03 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 47 HIS 0.006 0.001 HIS R 115 PHE 0.016 0.001 PHE R 253 TYR 0.021 0.001 TYR R 277 ARG 0.009 0.001 ARG L 7 *********************** 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 184 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: R 73 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7174 (ppp) REVERT: R 291 ASN cc_start: 0.8249 (t0) cc_final: 0.7806 (t0) REVERT: G 28 ILE cc_start: 0.8246 (mp) cc_final: 0.8013 (mp) outliers start: 28 outliers final: 17 residues processed: 169 average time/residue: 1.2512 time to fit residues: 225.2480 Evaluate side-chains 153 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 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 259 GLN Chi-restraints excluded: chain R residue 48 LEU 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 201 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 305 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 94 optimal weight: 0.0770 chunk 85 optimal weight: 0.0770 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8389 Z= 0.214 Angle : 0.761 12.642 11360 Z= 0.375 Chirality : 0.043 0.181 1291 Planarity : 0.004 0.041 1444 Dihedral : 4.756 50.365 1135 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.22 % Allowed : 23.53 % Favored : 73.25 % 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: 0.30 (0.26), residues: 1025 helix: 1.61 (0.26), residues: 397 sheet: -0.14 (0.33), residues: 247 loop : -1.03 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS R 115 PHE 0.014 0.001 PHE R 253 TYR 0.015 0.001 TYR L 1 ARG 0.008 0.001 ARG R 151 *********************** 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 180 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7113 (m-80) REVERT: R 55 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7382 (tp30) REVERT: R 291 ASN cc_start: 0.8336 (t0) cc_final: 0.7919 (t0) REVERT: G 28 ILE cc_start: 0.8286 (mp) cc_final: 0.8019 (mp) outliers start: 29 outliers final: 19 residues processed: 165 average time/residue: 1.2138 time to fit residues: 213.0724 Evaluate side-chains 156 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 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 259 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 59 VAL 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 R residue 217 HIS Chi-restraints excluded: chain R residue 305 GLU Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 R 308 ASN L 5 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8389 Z= 0.240 Angle : 0.781 15.390 11360 Z= 0.382 Chirality : 0.043 0.178 1291 Planarity : 0.004 0.042 1444 Dihedral : 4.749 50.161 1135 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.89 % Allowed : 24.75 % Favored : 72.36 % 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: 0.29 (0.26), residues: 1025 helix: 1.59 (0.26), residues: 397 sheet: -0.11 (0.33), residues: 247 loop : -1.04 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS R 115 PHE 0.019 0.001 PHE R 253 TYR 0.016 0.001 TYR L 1 ARG 0.009 0.001 ARG A 38 *********************** 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 168 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8581 (mm110) REVERT: B 234 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: G 28 ILE cc_start: 0.8291 (mp) cc_final: 0.8002 (mp) outliers start: 26 outliers final: 16 residues processed: 157 average time/residue: 1.1980 time to fit residues: 200.0462 Evaluate side-chains 148 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 51 LEU 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 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 305 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 0.0030 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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** B 75 GLN R 70 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8389 Z= 0.276 Angle : 0.815 16.032 11360 Z= 0.400 Chirality : 0.044 0.164 1291 Planarity : 0.005 0.084 1444 Dihedral : 4.894 50.463 1135 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.33 % Allowed : 25.08 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.26), residues: 1025 helix: 1.46 (0.26), residues: 401 sheet: -0.17 (0.33), residues: 239 loop : -1.00 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.003 0.001 HIS R 115 PHE 0.020 0.002 PHE B 292 TYR 0.016 0.001 TYR L 1 ARG 0.018 0.001 ARG R 65 ********************** 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 160 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 234 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7204 (m-80) REVERT: R 291 ASN cc_start: 0.8068 (t0) cc_final: 0.7712 (t0) REVERT: N 108 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7388 (m-80) outliers start: 21 outliers final: 16 residues processed: 147 average time/residue: 1.3468 time to fit residues: 210.1621 Evaluate side-chains 150 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 217 HIS Chi-restraints excluded: chain R residue 305 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 108 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.0770 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.129945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.093202 restraints weight = 16000.146| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.91 r_work: 0.3133 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8389 Z= 0.236 Angle : 0.833 15.778 11360 Z= 0.407 Chirality : 0.043 0.174 1291 Planarity : 0.004 0.057 1444 Dihedral : 4.838 49.576 1135 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.55 % Allowed : 25.19 % Favored : 72.25 % 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: 0.22 (0.26), residues: 1025 helix: 1.49 (0.26), residues: 397 sheet: -0.12 (0.32), residues: 249 loop : -1.07 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.009 0.001 HIS R 115 PHE 0.020 0.001 PHE R 253 TYR 0.019 0.001 TYR R 277 ARG 0.019 0.001 ARG R 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3962.16 seconds wall clock time: 71 minutes 33.12 seconds (4293.12 seconds total)