Starting phenix.real_space_refine on Fri Jul 19 16:36:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d68_30590/07_2024/7d68_30590.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d68_30590/07_2024/7d68_30590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d68_30590/07_2024/7d68_30590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d68_30590/07_2024/7d68_30590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d68_30590/07_2024/7d68_30590.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d68_30590/07_2024/7d68_30590.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 5447 2.51 5 N 1496 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "R ARG 171": "NH1" <-> "NH2" Residue "R ARG 242": "NH1" <-> "NH2" Residue "R GLU 281": "OE1" <-> "OE2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "R ARG 344": "NH1" <-> "NH2" Residue "R PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 382": "NH1" <-> "NH2" Residue "R ARG 453": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8564 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1885 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 249 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "R" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2426 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 8, 'TRANS': 283} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 5.02, per 1000 atoms: 0.59 Number of scatterers: 8564 At special positions: 0 Unit cell: (104.442, 95.316, 137.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1571 8.00 N 1496 7.00 C 5447 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 260 " - pdb=" SG CYS R 330 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.05 Conformation dependent library (CDL) restraints added in 1.6 seconds 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 41.1% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.978A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.764A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.792A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.922A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.753A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.685A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.990A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.616A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.718A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.533A pdb=" N PHE P 6 " --> pdb=" O ALA P 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 203 removed outlier: 3.844A pdb=" N ASP R 170 " --> pdb=" O LYS R 166 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU R 174 " --> pdb=" O ASP R 170 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 239 Processing helix chain 'R' and resid 252 through 257 removed outlier: 3.567A pdb=" N GLU R 255 " --> pdb=" O TYR R 252 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET R 256 " --> pdb=" O LEU R 253 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER R 257 " --> pdb=" O SER R 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 252 through 257' Processing helix chain 'R' and resid 258 through 288 removed outlier: 3.697A pdb=" N SER R 262 " --> pdb=" O THR R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 308 Processing helix chain 'R' and resid 311 through 325 Proline residue: R 317 - end of helix removed outlier: 3.855A pdb=" N ALA R 323 " --> pdb=" O GLY R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 371 Proline residue: R 346 - end of helix removed outlier: 4.074A pdb=" N CYS R 350 " --> pdb=" O PRO R 346 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN R 354 " --> pdb=" O CYS R 350 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA R 371 " --> pdb=" O SER R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 395 Proline residue: R 392 - end of helix Processing helix chain 'R' and resid 398 through 404 removed outlier: 3.557A pdb=" N PHE R 403 " --> pdb=" O ILE R 399 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE R 404 " --> pdb=" O LEU R 400 " (cutoff:3.500A) Processing helix chain 'R' and resid 411 through 437 removed outlier: 3.559A pdb=" N LEU R 415 " --> pdb=" O GLY R 411 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY R 429 " --> pdb=" O SER R 425 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE R 430 " --> pdb=" O SER R 426 " (cutoff:3.500A) Processing helix chain 'R' and resid 440 through 452 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.608A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.592A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.901A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.957A 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: 6.989A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.932A 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 151 removed outlier: 6.638A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.276A 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: 6.939A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.588A 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: 6.483A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.684A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.516A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 5.616A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1152 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: 2.50 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2187 1.33 - 1.45: 1828 1.45 - 1.58: 4652 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 8739 Sorted by residual: bond pdb=" C ARG R 210 " pdb=" O ARG R 210 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.17e-02 7.31e+03 4.48e+00 bond pdb=" C LEU R 206 " pdb=" O LEU R 206 " ideal model delta sigma weight residual 1.236 1.209 0.027 1.32e-02 5.74e+03 4.11e+00 bond pdb=" CA ALA A 226 " pdb=" C ALA A 226 " ideal model delta sigma weight residual 1.531 1.514 0.017 1.12e-02 7.97e+03 2.35e+00 bond pdb=" C TYR A 358 " pdb=" O TYR A 358 " ideal model delta sigma weight residual 1.234 1.215 0.018 1.22e-02 6.72e+03 2.29e+00 bond pdb=" C HIS A 357 " pdb=" O HIS A 357 " ideal model delta sigma weight residual 1.234 1.216 0.017 1.24e-02 6.50e+03 1.99e+00 ... (remaining 8734 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 187 106.95 - 113.72: 4844 113.72 - 120.50: 3521 120.50 - 127.27: 3179 127.27 - 134.04: 94 Bond angle restraints: 11825 Sorted by residual: angle pdb=" N ARG A 356 " pdb=" CA ARG A 356 " pdb=" C ARG A 356 " ideal model delta sigma weight residual 113.88 105.69 8.19 1.23e+00 6.61e-01 4.43e+01 angle pdb=" N HIS R 207 " pdb=" CA HIS R 207 " pdb=" C HIS R 207 " ideal model delta sigma weight residual 110.80 121.40 -10.60 2.13e+00 2.20e-01 2.48e+01 angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 112.04 106.17 5.87 1.44e+00 4.82e-01 1.66e+01 angle pdb=" N GLU R 442 " pdb=" CA GLU R 442 " pdb=" C GLU R 442 " ideal model delta sigma weight residual 111.28 115.36 -4.08 1.09e+00 8.42e-01 1.40e+01 angle pdb=" N SER R 402 " pdb=" CA SER R 402 " pdb=" C SER R 402 " ideal model delta sigma weight residual 111.28 107.40 3.88 1.09e+00 8.42e-01 1.27e+01 ... (remaining 11820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 4680 16.16 - 32.32: 401 32.32 - 48.48: 84 48.48 - 64.64: 17 64.64 - 80.80: 6 Dihedral angle restraints: 5188 sinusoidal: 2077 harmonic: 3111 Sorted by residual: dihedral pdb=" CB CYS R 260 " pdb=" SG CYS R 260 " pdb=" SG CYS R 330 " pdb=" CB CYS R 330 " ideal model delta sinusoidal sigma weight residual 93.00 40.15 52.85 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -158.23 -21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA LYS A 216 " pdb=" C LYS A 216 " pdb=" N VAL A 217 " pdb=" CA VAL A 217 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 5185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1205 0.080 - 0.159: 109 0.159 - 0.239: 2 0.239 - 0.318: 0 0.318 - 0.398: 1 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CA HIS R 207 " pdb=" N HIS R 207 " pdb=" C HIS R 207 " pdb=" CB HIS R 207 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA ASP A 354 " pdb=" N ASP A 354 " pdb=" C ASP A 354 " pdb=" CB ASP A 354 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE R 404 " pdb=" N ILE R 404 " pdb=" C ILE R 404 " pdb=" CB ILE R 404 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1314 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 345 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO R 346 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 346 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 346 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.014 2.00e-02 2.50e+03 1.37e-02 3.74e+00 pdb=" CG TYR B 59 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 350 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C THR A 350 " 0.029 2.00e-02 2.50e+03 pdb=" O THR A 350 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A 351 " -0.010 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 137 2.68 - 3.23: 8179 3.23 - 3.79: 12857 3.79 - 4.34: 17957 4.34 - 4.90: 30124 Nonbonded interactions: 69254 Sorted by model distance: nonbonded pdb=" OD1 ASN A 292 " pdb=" OG1 THR A 364 " model vdw 2.121 2.440 nonbonded pdb=" NH1 ARG B 22 " pdb=" O ALA B 257 " model vdw 2.210 2.520 nonbonded pdb=" ND2 ASN N 35 " pdb=" OD2 ASP N 109 " model vdw 2.232 2.520 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.238 2.520 nonbonded pdb=" OE1 GLU R 281 " pdb=" O HOH R 701 " model vdw 2.244 2.440 ... (remaining 69249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.500 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8739 Z= 0.263 Angle : 0.664 10.598 11825 Z= 0.395 Chirality : 0.045 0.398 1317 Planarity : 0.004 0.050 1503 Dihedral : 13.068 80.805 3170 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 0.76 % Allowed : 3.89 % Favored : 95.36 % 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: -2.09 (0.23), residues: 1052 helix: -0.47 (0.23), residues: 390 sheet: -1.37 (0.32), residues: 220 loop : -2.17 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 99 HIS 0.007 0.001 HIS B 62 PHE 0.015 0.002 PHE A 222 TYR 0.034 0.002 TYR B 59 ARG 0.006 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.6966 (tm-30) cc_final: 0.6675 (tm-30) REVERT: A 341 ILE cc_start: 0.7881 (mm) cc_final: 0.7526 (mm) REVERT: A 373 ARG cc_start: 0.7304 (mmm160) cc_final: 0.7072 (mmt180) REVERT: R 215 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7586 (mtp) REVERT: R 338 LYS cc_start: 0.7552 (mttm) cc_final: 0.6846 (tttp) outliers start: 7 outliers final: 2 residues processed: 157 average time/residue: 1.2931 time to fit residues: 215.5875 Evaluate side-chains 124 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain P residue 1 HIS Chi-restraints excluded: chain R residue 215 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 371 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 239 ASN N 77 ASN ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 372 HIS R 408 GLN R 440 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8739 Z= 0.226 Angle : 0.583 7.384 11825 Z= 0.305 Chirality : 0.042 0.153 1317 Planarity : 0.004 0.052 1503 Dihedral : 4.943 31.712 1176 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.62 % Allowed : 12.53 % Favored : 85.85 % 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: -0.96 (0.25), residues: 1052 helix: 0.72 (0.25), residues: 407 sheet: -0.84 (0.33), residues: 212 loop : -1.84 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.006 0.001 HIS B 62 PHE 0.018 0.002 PHE R 202 TYR 0.027 0.001 TYR R 182 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.6983 (tm-30) cc_final: 0.6642 (tm-30) REVERT: A 268 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: A 341 ILE cc_start: 0.7792 (mm) cc_final: 0.7539 (mm) REVERT: B 270 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7701 (pp) REVERT: R 326 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.5482 (mp0) REVERT: R 338 LYS cc_start: 0.7579 (mttm) cc_final: 0.6842 (tttp) outliers start: 15 outliers final: 4 residues processed: 129 average time/residue: 1.2101 time to fit residues: 166.4138 Evaluate side-chains 125 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 292 THR Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 326 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 35 GLN A 294 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 239 ASN R 245 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8739 Z= 0.216 Angle : 0.551 6.628 11825 Z= 0.289 Chirality : 0.042 0.169 1317 Planarity : 0.004 0.057 1503 Dihedral : 4.500 21.759 1170 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.27 % Allowed : 15.12 % Favored : 82.61 % 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: -0.51 (0.25), residues: 1052 helix: 1.16 (0.26), residues: 412 sheet: -0.63 (0.34), residues: 213 loop : -1.68 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.003 0.001 HIS B 62 PHE 0.021 0.002 PHE R 202 TYR 0.025 0.001 TYR R 182 ARG 0.007 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7626 (pttm) REVERT: A 221 MET cc_start: 0.8619 (ttp) cc_final: 0.8282 (ttt) REVERT: A 268 GLU cc_start: 0.7171 (mp0) cc_final: 0.6753 (mp0) REVERT: A 341 ILE cc_start: 0.7770 (mm) cc_final: 0.7507 (mm) REVERT: B 59 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: B 262 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7023 (mpt) REVERT: B 270 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7774 (pp) REVERT: B 290 ASP cc_start: 0.7691 (m-30) cc_final: 0.7391 (m-30) REVERT: N 20 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7369 (mm) REVERT: R 302 ARG cc_start: 0.6697 (mtp180) cc_final: 0.6389 (mmt-90) REVERT: R 326 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.5461 (mp0) REVERT: R 338 LYS cc_start: 0.7585 (mttm) cc_final: 0.6825 (tttp) REVERT: R 412 PHE cc_start: 0.6342 (OUTLIER) cc_final: 0.5164 (t80) outliers start: 21 outliers final: 5 residues processed: 128 average time/residue: 1.1668 time to fit residues: 159.5077 Evaluate side-chains 128 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 292 THR Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 412 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8739 Z= 0.163 Angle : 0.523 8.138 11825 Z= 0.273 Chirality : 0.040 0.145 1317 Planarity : 0.004 0.056 1503 Dihedral : 4.299 21.287 1170 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.16 % Allowed : 17.17 % Favored : 80.67 % 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: -0.20 (0.26), residues: 1052 helix: 1.33 (0.26), residues: 423 sheet: -0.48 (0.34), residues: 212 loop : -1.47 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.002 0.001 HIS P 1 PHE 0.023 0.001 PHE R 202 TYR 0.022 0.001 TYR R 182 ARG 0.004 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.995 Fit side-chains REVERT: A 221 MET cc_start: 0.8616 (ttp) cc_final: 0.8312 (ttt) REVERT: A 341 ILE cc_start: 0.7739 (mm) cc_final: 0.7471 (mm) REVERT: B 59 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: B 262 MET cc_start: 0.7404 (mpp) cc_final: 0.7026 (mpt) REVERT: B 270 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7770 (pp) REVERT: B 290 ASP cc_start: 0.7655 (m-30) cc_final: 0.7368 (m-30) REVERT: R 302 ARG cc_start: 0.6680 (mtp180) cc_final: 0.6371 (mmt-90) REVERT: R 326 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.5451 (mp0) REVERT: R 338 LYS cc_start: 0.7640 (mttm) cc_final: 0.6881 (tttp) REVERT: R 412 PHE cc_start: 0.6315 (OUTLIER) cc_final: 0.5126 (t80) outliers start: 20 outliers final: 6 residues processed: 126 average time/residue: 1.1443 time to fit residues: 154.2707 Evaluate side-chains 122 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 412 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.0670 chunk 90 optimal weight: 0.6980 chunk 25 optimal weight: 0.0040 chunk 33 optimal weight: 2.9990 overall best weight: 0.4930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** P 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 245 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8739 Z= 0.150 Angle : 0.499 7.199 11825 Z= 0.261 Chirality : 0.039 0.142 1317 Planarity : 0.004 0.055 1503 Dihedral : 4.084 20.197 1170 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.94 % Allowed : 18.36 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1052 helix: 1.56 (0.26), residues: 423 sheet: -0.10 (0.35), residues: 198 loop : -1.48 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.002 0.000 HIS P 1 PHE 0.027 0.001 PHE R 202 TYR 0.020 0.001 TYR R 182 ARG 0.004 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.8566 (ttp) cc_final: 0.8247 (ttt) REVERT: A 341 ILE cc_start: 0.7688 (mm) cc_final: 0.7397 (mm) REVERT: B 13 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6496 (mp10) REVERT: B 59 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: B 61 MET cc_start: 0.8807 (pp-130) cc_final: 0.8539 (ppp) REVERT: B 220 GLN cc_start: 0.7902 (mt0) cc_final: 0.7466 (mt0) REVERT: B 262 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.7015 (mpt) REVERT: B 270 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7766 (pp) REVERT: B 290 ASP cc_start: 0.7552 (m-30) cc_final: 0.7295 (m-30) REVERT: R 302 ARG cc_start: 0.6675 (mtp180) cc_final: 0.6369 (mmt-90) REVERT: R 326 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.5446 (mp0) REVERT: R 338 LYS cc_start: 0.7655 (mttm) cc_final: 0.6875 (tttp) REVERT: R 412 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.4854 (t80) outliers start: 18 outliers final: 7 residues processed: 127 average time/residue: 1.2330 time to fit residues: 168.2301 Evaluate side-chains 133 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 412 PHE Chi-restraints excluded: chain R residue 452 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 24 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.0040 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8739 Z= 0.301 Angle : 0.584 8.474 11825 Z= 0.305 Chirality : 0.043 0.168 1317 Planarity : 0.004 0.058 1503 Dihedral : 4.366 19.564 1170 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.59 % Allowed : 19.22 % Favored : 78.19 % 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: -0.19 (0.26), residues: 1052 helix: 1.39 (0.26), residues: 415 sheet: -0.50 (0.34), residues: 213 loop : -1.45 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.004 0.001 HIS G 44 PHE 0.024 0.002 PHE R 202 TYR 0.024 0.002 TYR R 182 ARG 0.003 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.913 Fit side-chains REVERT: A 341 ILE cc_start: 0.7724 (mm) cc_final: 0.7369 (mm) REVERT: A 373 ARG cc_start: 0.7351 (mmm160) cc_final: 0.6979 (tpt170) REVERT: B 59 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8371 (m-80) REVERT: B 61 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8628 (ppp) REVERT: B 270 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7789 (pp) REVERT: B 290 ASP cc_start: 0.7624 (m-30) cc_final: 0.7410 (m-30) REVERT: R 302 ARG cc_start: 0.6626 (mtp180) cc_final: 0.6343 (mmt-90) REVERT: R 326 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.5494 (mp0) outliers start: 24 outliers final: 13 residues processed: 124 average time/residue: 1.1255 time to fit residues: 149.3323 Evaluate side-chains 132 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 292 THR Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 452 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 88 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN R 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8739 Z= 0.185 Angle : 0.522 7.244 11825 Z= 0.274 Chirality : 0.040 0.143 1317 Planarity : 0.004 0.061 1503 Dihedral : 4.198 19.516 1170 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.02 % Allowed : 19.33 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1052 helix: 1.63 (0.26), residues: 413 sheet: -0.40 (0.34), residues: 210 loop : -1.41 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.002 0.001 HIS A 357 PHE 0.025 0.001 PHE R 202 TYR 0.021 0.001 TYR R 182 ARG 0.003 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 0.938 Fit side-chains REVERT: A 221 MET cc_start: 0.8630 (ttp) cc_final: 0.8304 (ttt) REVERT: A 341 ILE cc_start: 0.7731 (mm) cc_final: 0.7384 (mm) REVERT: B 59 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: B 61 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8584 (ppp) REVERT: B 262 MET cc_start: 0.7535 (mpp) cc_final: 0.7255 (mpt) REVERT: B 270 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7837 (pp) REVERT: R 302 ARG cc_start: 0.6613 (mtp180) cc_final: 0.6346 (mmt-90) REVERT: R 326 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.5461 (mp0) REVERT: R 338 LYS cc_start: 0.7655 (mttm) cc_final: 0.6856 (tttp) outliers start: 28 outliers final: 13 residues processed: 130 average time/residue: 1.1541 time to fit residues: 161.0725 Evaluate side-chains 127 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 362 LEU Chi-restraints excluded: chain R residue 412 PHE Chi-restraints excluded: chain R residue 452 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 88 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8739 Z= 0.255 Angle : 0.558 7.482 11825 Z= 0.292 Chirality : 0.041 0.147 1317 Planarity : 0.004 0.060 1503 Dihedral : 4.273 19.050 1170 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.13 % Allowed : 19.55 % Favored : 77.32 % 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: -0.07 (0.26), residues: 1052 helix: 1.54 (0.26), residues: 414 sheet: -0.30 (0.34), residues: 204 loop : -1.50 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.003 0.001 HIS G 44 PHE 0.026 0.002 PHE R 202 TYR 0.024 0.002 TYR R 182 ARG 0.003 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 0.987 Fit side-chains REVERT: A 221 MET cc_start: 0.8647 (ttp) cc_final: 0.8308 (ttt) REVERT: A 341 ILE cc_start: 0.7725 (mm) cc_final: 0.7368 (mm) REVERT: B 59 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: B 61 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8591 (ppp) REVERT: B 262 MET cc_start: 0.7611 (mpp) cc_final: 0.7296 (mpt) REVERT: B 270 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7985 (pp) REVERT: R 302 ARG cc_start: 0.6608 (mtp180) cc_final: 0.6329 (mmt-90) REVERT: R 326 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.5488 (mp0) outliers start: 29 outliers final: 17 residues processed: 129 average time/residue: 1.1003 time to fit residues: 152.2339 Evaluate side-chains 131 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 292 THR Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 362 LEU Chi-restraints excluded: chain R residue 452 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 88 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8739 Z= 0.222 Angle : 0.540 7.225 11825 Z= 0.282 Chirality : 0.041 0.143 1317 Planarity : 0.004 0.061 1503 Dihedral : 4.217 18.868 1170 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.24 % Allowed : 19.76 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1052 helix: 1.62 (0.26), residues: 414 sheet: -0.26 (0.34), residues: 204 loop : -1.45 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 99 HIS 0.002 0.001 HIS G 44 PHE 0.029 0.002 PHE R 202 TYR 0.023 0.001 TYR R 182 ARG 0.003 0.000 ARG R 344 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 0.847 Fit side-chains REVERT: A 221 MET cc_start: 0.8649 (ttp) cc_final: 0.8331 (ttt) REVERT: A 341 ILE cc_start: 0.7721 (mm) cc_final: 0.7371 (mm) REVERT: B 61 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8583 (ppp) REVERT: B 220 GLN cc_start: 0.7937 (mt0) cc_final: 0.7528 (mt0) REVERT: B 270 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8021 (pp) REVERT: R 326 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.5475 (mp0) outliers start: 30 outliers final: 19 residues processed: 129 average time/residue: 1.1147 time to fit residues: 154.0557 Evaluate side-chains 133 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 292 THR Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 362 LEU Chi-restraints excluded: chain R residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8739 Z= 0.188 Angle : 0.523 6.888 11825 Z= 0.275 Chirality : 0.040 0.142 1317 Planarity : 0.004 0.060 1503 Dihedral : 4.138 18.849 1170 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.48 % Allowed : 20.19 % Favored : 77.32 % 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: 0.14 (0.26), residues: 1052 helix: 1.74 (0.26), residues: 415 sheet: -0.18 (0.34), residues: 204 loop : -1.43 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.003 0.001 HIS A 357 PHE 0.030 0.001 PHE R 202 TYR 0.021 0.001 TYR R 182 ARG 0.003 0.000 ARG R 344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.946 Fit side-chains REVERT: A 12 GLN cc_start: 0.7370 (tm-30) cc_final: 0.6881 (tm-30) REVERT: A 31 GLN cc_start: 0.6835 (mm-40) cc_final: 0.6282 (tp-100) REVERT: A 221 MET cc_start: 0.8642 (ttp) cc_final: 0.8326 (ttt) REVERT: A 341 ILE cc_start: 0.7704 (mm) cc_final: 0.7373 (mm) REVERT: B 61 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8556 (ppp) REVERT: B 220 GLN cc_start: 0.7918 (mt0) cc_final: 0.7503 (mt0) REVERT: B 270 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8086 (pp) REVERT: R 326 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.5466 (mp0) REVERT: R 338 LYS cc_start: 0.7677 (mttm) cc_final: 0.6897 (tttp) outliers start: 23 outliers final: 16 residues processed: 125 average time/residue: 1.1113 time to fit residues: 149.2785 Evaluate side-chains 130 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 260 CYS Chi-restraints excluded: chain R residue 292 THR Chi-restraints excluded: chain R residue 326 GLU Chi-restraints excluded: chain R residue 362 LEU Chi-restraints excluded: chain R residue 452 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 22 optimal weight: 30.0000 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 1 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.186723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146869 restraints weight = 9648.028| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.21 r_work: 0.3524 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8739 Z= 0.173 Angle : 0.519 6.791 11825 Z= 0.271 Chirality : 0.041 0.281 1317 Planarity : 0.004 0.060 1503 Dihedral : 4.094 18.694 1170 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.48 % Allowed : 20.41 % Favored : 77.11 % 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: 0.25 (0.26), residues: 1052 helix: 1.86 (0.26), residues: 415 sheet: -0.13 (0.34), residues: 204 loop : -1.39 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.003 0.001 HIS A 357 PHE 0.032 0.001 PHE R 202 TYR 0.020 0.001 TYR R 182 ARG 0.002 0.000 ARG R 344 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3464.90 seconds wall clock time: 61 minutes 8.64 seconds (3668.64 seconds total)