Starting phenix.real_space_refine on Fri Sep 11 10:41:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vcb_21147/09_2026/6vcb_21147_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vcb_21147/09_2026/6vcb_21147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vcb_21147/09_2026/6vcb_21147_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vcb_21147/09_2026/6vcb_21147_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vcb_21147/09_2026/6vcb_21147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vcb_21147/09_2026/6vcb_21147.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 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 S 54 5.16 5 Cl 2 4.86 5 C 5787 2.51 5 N 1573 2.21 5 O 1658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9074 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3000 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 14, 'TRANS': 363} Chain breaks: 3 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 5, 'GLU:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 231 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1810 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 5 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'QW7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.72, per 1000 atoms: 0.19 Number of scatterers: 9074 At special positions: 0 Unit cell: (166.4, 102.96, 98.8, 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) Cl 2 17.00 S 54 16.00 O 1658 8.00 N 1573 7.00 C 5787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 0.68 Conformation dependent library (CDL) restraints added in 282.8 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 42.1% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'R' and resid 31 through 51 removed outlier: 3.917A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 93 removed outlier: 4.439A pdb=" N SER R 93 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 168 removed outlier: 3.681A pdb=" N LEU R 142 " --> pdb=" O GLU R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 206 Processing helix chain 'R' and resid 216 through 223 removed outlier: 3.898A pdb=" N ASP R 222 " --> pdb=" O LEU R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 256 Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.638A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 291 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 303 through 336 removed outlier: 4.504A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 368 removed outlier: 3.691A pdb=" N ALA R 368 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 393 removed outlier: 4.028A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 402 Processing helix chain 'R' and resid 406 through 421 Processing helix chain 'P' and resid 8 through 34 removed outlier: 3.681A pdb=" N LYS P 34 " --> pdb=" O ALA P 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 38 Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.770A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.115A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.836A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.587A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.575A pdb=" N GLN B 32 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 4.116A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.646A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.606A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.094A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'R' and resid 79 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.861A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.747A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.040A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.741A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.707A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.495A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.259A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.450A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1314 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: 1.52 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2908 1.34 - 1.46: 2128 1.46 - 1.58: 4167 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 9277 Sorted by residual: bond pdb=" C17 QW7 R 501 " pdb=" C18 QW7 R 501 " ideal model delta sigma weight residual 1.490 1.391 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CG LEU R 159 " pdb=" CD1 LEU R 159 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.06e+00 bond pdb=" C03 QW7 R 501 " pdb=" O02 QW7 R 501 " ideal model delta sigma weight residual 1.349 1.400 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" CG LEU R 159 " pdb=" CD2 LEU R 159 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.08e+00 bond pdb=" C26 QW7 R 501 " pdb=" C27 QW7 R 501 " ideal model delta sigma weight residual 1.528 1.483 0.045 2.00e-02 2.50e+03 5.02e+00 ... (remaining 9272 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 12449 3.65 - 7.30: 125 7.30 - 10.95: 16 10.95 - 14.60: 2 14.60 - 18.25: 1 Bond angle restraints: 12593 Sorted by residual: angle pdb=" CA LEU A 46 " pdb=" CB LEU A 46 " pdb=" CG LEU A 46 " ideal model delta sigma weight residual 116.30 134.55 -18.25 3.50e+00 8.16e-02 2.72e+01 angle pdb=" C ARG R 299 " pdb=" N ASN R 300 " pdb=" CA ASN R 300 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 130.74 -14.44 3.50e+00 8.16e-02 1.70e+01 angle pdb=" C ILE R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.14 114.24 6.90 1.75e+00 3.27e-01 1.56e+01 ... (remaining 12588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 5047 15.42 - 30.84: 317 30.84 - 46.26: 89 46.26 - 61.68: 12 61.68 - 77.11: 8 Dihedral angle restraints: 5473 sinusoidal: 2106 harmonic: 3367 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -152.86 66.86 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 145.59 -52.59 1 1.00e+01 1.00e-02 3.77e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 5470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1046 0.063 - 0.126: 305 0.126 - 0.190: 36 0.190 - 0.253: 12 0.253 - 0.316: 5 Chirality restraints: 1404 Sorted by residual: chirality pdb=" C09 QW7 R 501 " pdb=" C08 QW7 R 501 " pdb=" C10 QW7 R 501 " pdb=" N11 QW7 R 501 " both_signs ideal model delta sigma weight residual False -2.29 -2.60 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CG LEU A 44 " pdb=" CB LEU A 44 " pdb=" CD1 LEU A 44 " pdb=" CD2 LEU A 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CG LEU R 183 " pdb=" CB LEU R 183 " pdb=" CD1 LEU R 183 " pdb=" CD2 LEU R 183 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1401 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 242 " -0.018 2.00e-02 2.50e+03 1.75e-02 6.10e+00 pdb=" CG TYR R 242 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR R 242 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR R 242 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR R 242 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR R 242 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 242 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 242 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 169 " 0.021 2.00e-02 2.50e+03 1.50e-02 5.63e+00 pdb=" CG TRP B 169 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 169 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 169 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 169 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 169 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 169 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 282 " -0.039 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO R 283 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " -0.033 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 192 2.67 - 3.23: 8324 3.23 - 3.79: 14865 3.79 - 4.34: 19328 4.34 - 4.90: 31834 Nonbonded interactions: 74543 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.117 3.040 nonbonded pdb=" OD2 ASP B 212 " pdb=" NH2 ARG B 219 " model vdw 2.145 3.120 nonbonded pdb=" OE2 GLU N 6 " pdb=" N GLY N 121 " model vdw 2.159 3.120 nonbonded pdb=" NE2 HIS A 362 " pdb=" OD2 ASP A 378 " model vdw 2.160 3.120 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.222 3.040 ... (remaining 74538 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.540 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 0.099 9283 Z= 0.284 Angle : 1.007 18.255 12605 Z= 0.532 Chirality : 0.061 0.316 1404 Planarity : 0.007 0.058 1599 Dihedral : 11.588 77.105 3275 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.85 % Allowed : 5.32 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.19), residues: 1130 helix: -2.61 (0.17), residues: 456 sheet: -2.38 (0.30), residues: 218 loop : -3.17 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 118 TYR 0.041 0.004 TYR R 242 PHE 0.021 0.003 PHE R 280 TRP 0.041 0.004 TRP B 169 HIS 0.010 0.002 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.28 ( 9277) covalent geometry : angle 1.00638 / 0.53 (12593) SS BOND : bond 0.00437 / 0.22 ( 6) SS BOND : angle 1.77997 / 1.03 ( 12) hydrogen bonds : bond 0.11091 / 8.10 ( 464) hydrogen bonds : angle 6.70915 / 4.69 ( 1314) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 267 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7641 (tp30) cc_final: 0.7356 (mt-10) REVERT: R 304 ASN cc_start: 0.7541 (m-40) cc_final: 0.6142 (t0) REVERT: R 372 ASP cc_start: 0.8600 (m-30) cc_final: 0.7945 (m-30) REVERT: R 417 TRP cc_start: 0.6373 (t-100) cc_final: 0.6064 (t-100) REVERT: P 18 SER cc_start: 0.8125 (m) cc_final: 0.7828 (p) REVERT: P 27 GLU cc_start: 0.7702 (tt0) cc_final: 0.7384 (tt0) REVERT: A 338 LYS cc_start: 0.8594 (ttpm) cc_final: 0.8278 (ttpp) REVERT: B 211 TRP cc_start: 0.8795 (m100) cc_final: 0.8570 (m100) REVERT: B 335 PHE cc_start: 0.7892 (m-80) cc_final: 0.7673 (m-10) REVERT: G 19 LEU cc_start: 0.8822 (mt) cc_final: 0.8493 (mt) REVERT: G 46 LYS cc_start: 0.8561 (mppt) cc_final: 0.8351 (mmtm) REVERT: G 48 ASP cc_start: 0.8561 (t70) cc_final: 0.8201 (t0) REVERT: N 82 GLN cc_start: 0.7274 (tp-100) cc_final: 0.7039 (tp-100) REVERT: N 105 ARG cc_start: 0.6366 (mtp-110) cc_final: 0.6160 (mtp-110) outliers start: 8 outliers final: 4 residues processed: 274 average time/residue: 0.1208 time to fit residues: 43.5472 Evaluate side-chains 172 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 168 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain A residue 43 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 chunk 5 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.2695 > 50:) chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 45 GLN R 47 GLN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 210 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN R 374 HIS A 14 ASN A 264 ASN A 267 GLN B 155 ASN B 266 HIS N 5 GLN N 120 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.159965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125565 restraints weight = 12580.748| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.63 r_work: 0.3483 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9283 Z= 0.154 Angle : 0.662 12.384 12605 Z= 0.345 Chirality : 0.045 0.168 1404 Planarity : 0.005 0.038 1599 Dihedral : 6.089 51.306 1286 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.41 % Allowed : 11.61 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.22), residues: 1130 helix: -0.79 (0.22), residues: 472 sheet: -2.11 (0.31), residues: 199 loop : -2.81 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 310 TYR 0.018 0.002 TYR R 148 PHE 0.022 0.002 PHE R 280 TRP 0.033 0.002 TRP R 297 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 9277) covalent geometry : angle 0.66161 / 0.34 (12593) SS BOND : bond 0.00333 / 0.18 ( 6) SS BOND : angle 0.96396 / 0.57 ( 12) hydrogen bonds : bond 0.04290 / 2.82 ( 464) hydrogen bonds : angle 5.33775 / 3.77 ( 1314) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7950 (tp30) cc_final: 0.7269 (mt-10) REVERT: R 299 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7719 (mmm160) REVERT: R 302 ASN cc_start: 0.8201 (t0) cc_final: 0.7999 (t0) REVERT: R 304 ASN cc_start: 0.7360 (m-40) cc_final: 0.5940 (t0) REVERT: B 10 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8176 (tm-30) REVERT: B 12 GLU cc_start: 0.8620 (tp30) cc_final: 0.8408 (tp30) REVERT: B 14 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8141 (tp) REVERT: B 85 TYR cc_start: 0.7456 (m-80) cc_final: 0.7215 (m-10) REVERT: B 211 TRP cc_start: 0.9011 (m100) cc_final: 0.8746 (m100) REVERT: B 219 ARG cc_start: 0.8383 (ptp-110) cc_final: 0.8096 (ptp-170) REVERT: B 334 SER cc_start: 0.8599 (m) cc_final: 0.8097 (t) REVERT: G 48 ASP cc_start: 0.8489 (t70) cc_final: 0.8213 (t0) REVERT: N 82 GLN cc_start: 0.7511 (tp-100) cc_final: 0.7152 (tp-100) REVERT: N 83 MET cc_start: 0.7167 (mtt) cc_final: 0.6744 (mtt) REVERT: N 98 ARG cc_start: 0.8422 (ptt90) cc_final: 0.8126 (ptt90) outliers start: 32 outliers final: 21 residues processed: 224 average time/residue: 0.0955 time to fit residues: 29.5688 Evaluate side-chains 194 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 210 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN A 357 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.158710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124120 restraints weight = 12528.386| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.63 r_work: 0.3461 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9283 Z= 0.150 Angle : 0.636 9.706 12605 Z= 0.328 Chirality : 0.044 0.214 1404 Planarity : 0.004 0.034 1599 Dihedral : 5.662 55.830 1286 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.30 % Allowed : 14.48 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.23), residues: 1130 helix: 0.07 (0.24), residues: 471 sheet: -1.97 (0.31), residues: 213 loop : -2.51 (0.25), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 310 TYR 0.015 0.002 TYR R 242 PHE 0.029 0.002 PHE B 199 TRP 0.030 0.002 TRP R 297 HIS 0.005 0.001 HIS R 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 9277) covalent geometry : angle 0.63535 / 0.33 (12593) SS BOND : bond 0.00215 / 0.11 ( 6) SS BOND : angle 0.99787 / 0.57 ( 12) hydrogen bonds : bond 0.03990 / 2.59 ( 464) hydrogen bonds : angle 4.95482 / 3.52 ( 1314) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7981 (tp30) cc_final: 0.7216 (pm20) REVERT: R 289 TYR cc_start: 0.8331 (t80) cc_final: 0.7862 (t80) REVERT: R 304 ASN cc_start: 0.7349 (m-40) cc_final: 0.5962 (t0) REVERT: R 369 PHE cc_start: 0.4840 (t80) cc_final: 0.3814 (t80) REVERT: R 373 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: A 270 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8692 (mp) REVERT: A 310 ASP cc_start: 0.7170 (m-30) cc_final: 0.6889 (p0) REVERT: A 338 LYS cc_start: 0.8412 (ttpm) cc_final: 0.7986 (ttpp) REVERT: B 10 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 12 GLU cc_start: 0.8707 (tp30) cc_final: 0.8451 (tp30) REVERT: B 219 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.8043 (ptp-170) REVERT: B 256 ARG cc_start: 0.8101 (mtm180) cc_final: 0.7849 (mtm110) REVERT: B 334 SER cc_start: 0.8652 (m) cc_final: 0.8181 (t) REVERT: N 82 GLN cc_start: 0.7424 (tp-100) cc_final: 0.7192 (tp-100) REVERT: N 118 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.8538 (mtm-85) outliers start: 31 outliers final: 19 residues processed: 217 average time/residue: 0.1037 time to fit residues: 30.6554 Evaluate side-chains 182 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 2 optimal weight: 0.0030 chunk 75 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.161520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127761 restraints weight = 12559.923| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.75 r_work: 0.3494 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9283 Z= 0.117 Angle : 0.580 8.034 12605 Z= 0.301 Chirality : 0.043 0.235 1404 Planarity : 0.004 0.060 1599 Dihedral : 4.966 37.238 1284 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.05 % Allowed : 15.23 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.24), residues: 1130 helix: 0.55 (0.24), residues: 472 sheet: -1.72 (0.32), residues: 221 loop : -2.21 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 8 TYR 0.015 0.001 TYR R 88 PHE 0.020 0.001 PHE B 199 TRP 0.021 0.001 TRP R 297 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 9277) covalent geometry : angle 0.57983 / 0.30 (12593) SS BOND : bond 0.00173 / 0.11 ( 6) SS BOND : angle 0.98377 / 0.58 ( 12) hydrogen bonds : bond 0.03707 / 2.40 ( 464) hydrogen bonds : angle 4.72093 / 3.35 ( 1314) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 41 GLU cc_start: 0.8758 (tp30) cc_final: 0.8098 (tp30) REVERT: R 262 GLU cc_start: 0.7847 (tp30) cc_final: 0.7215 (pm20) REVERT: R 291 TYR cc_start: 0.7861 (m-10) cc_final: 0.7657 (m-10) REVERT: R 304 ASN cc_start: 0.7458 (m-40) cc_final: 0.6035 (t0) REVERT: R 369 PHE cc_start: 0.4888 (t80) cc_final: 0.3868 (t80) REVERT: R 373 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: R 418 GLU cc_start: 0.7138 (tp30) cc_final: 0.6593 (mt-10) REVERT: A 270 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8669 (mp) REVERT: A 310 ASP cc_start: 0.7144 (m-30) cc_final: 0.6896 (p0) REVERT: A 338 LYS cc_start: 0.8371 (ttpm) cc_final: 0.8156 (ttpp) REVERT: A 360 TYR cc_start: 0.8805 (m-10) cc_final: 0.8588 (m-10) REVERT: B 10 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8051 (tm-30) REVERT: B 12 GLU cc_start: 0.8748 (tp30) cc_final: 0.8477 (tp30) REVERT: B 211 TRP cc_start: 0.8943 (m100) cc_final: 0.8575 (m100) REVERT: B 256 ARG cc_start: 0.8033 (mtm180) cc_final: 0.7776 (mtm110) REVERT: N 32 TYR cc_start: 0.8080 (m-10) cc_final: 0.7790 (m-80) outliers start: 38 outliers final: 21 residues processed: 203 average time/residue: 0.0917 time to fit residues: 26.0865 Evaluate side-chains 191 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 371 MET Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS B 9 GLN B 295 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.160216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126537 restraints weight = 12571.552| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.77 r_work: 0.3479 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9283 Z= 0.125 Angle : 0.585 10.214 12605 Z= 0.301 Chirality : 0.043 0.242 1404 Planarity : 0.004 0.073 1599 Dihedral : 4.778 36.810 1283 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.73 % Allowed : 17.15 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.25), residues: 1130 helix: 0.78 (0.25), residues: 473 sheet: -1.57 (0.33), residues: 221 loop : -2.07 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 98 TYR 0.012 0.001 TYR R 148 PHE 0.017 0.001 PHE B 199 TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9277) covalent geometry : angle 0.58484 / 0.30 (12593) SS BOND : bond 0.00212 / 0.13 ( 6) SS BOND : angle 0.82537 / 0.44 ( 12) hydrogen bonds : bond 0.03674 / 2.36 ( 464) hydrogen bonds : angle 4.63323 / 3.29 ( 1314) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 41 GLU cc_start: 0.8769 (tp30) cc_final: 0.8168 (tp30) REVERT: R 262 GLU cc_start: 0.7870 (tp30) cc_final: 0.7257 (pm20) REVERT: R 289 TYR cc_start: 0.8163 (t80) cc_final: 0.7740 (t80) REVERT: R 291 TYR cc_start: 0.7889 (m-10) cc_final: 0.7684 (m-10) REVERT: R 304 ASN cc_start: 0.7527 (m-40) cc_final: 0.6128 (t0) REVERT: R 369 PHE cc_start: 0.5059 (t80) cc_final: 0.3966 (t80) REVERT: R 373 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: R 418 GLU cc_start: 0.7176 (tp30) cc_final: 0.6630 (mt-10) REVERT: A 270 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8677 (mp) REVERT: A 338 LYS cc_start: 0.8446 (ttpm) cc_final: 0.8109 (ttpp) REVERT: A 360 TYR cc_start: 0.8798 (m-10) cc_final: 0.8493 (m-10) REVERT: B 10 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 12 GLU cc_start: 0.8805 (tp30) cc_final: 0.8553 (tp30) REVERT: B 211 TRP cc_start: 0.8958 (m100) cc_final: 0.8519 (m100) REVERT: B 256 ARG cc_start: 0.7932 (mtm180) cc_final: 0.7704 (mtm180) REVERT: G 48 ASP cc_start: 0.8799 (t0) cc_final: 0.8521 (t0) REVERT: N 32 TYR cc_start: 0.8075 (m-10) cc_final: 0.7780 (m-80) REVERT: N 98 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8620 (ptt-90) outliers start: 35 outliers final: 21 residues processed: 204 average time/residue: 0.0955 time to fit residues: 27.3547 Evaluate side-chains 191 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 98 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 94 optimal weight: 0.0670 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 221 GLN P 23 GLN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.152679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118555 restraints weight = 12714.566| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.64 r_work: 0.3369 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9283 Z= 0.257 Angle : 0.699 11.092 12605 Z= 0.362 Chirality : 0.048 0.253 1404 Planarity : 0.005 0.074 1599 Dihedral : 5.172 36.244 1283 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.15 % Allowed : 18.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.24), residues: 1130 helix: 0.62 (0.24), residues: 465 sheet: -1.85 (0.33), residues: 204 loop : -1.78 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 98 TYR 0.024 0.002 TYR R 242 PHE 0.018 0.002 PHE B 199 TRP 0.038 0.002 TRP R 297 HIS 0.007 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.26 ( 9277) covalent geometry : angle 0.69822 / 0.36 (12593) SS BOND : bond 0.00234 / 0.14 ( 6) SS BOND : angle 0.97720 / 0.53 ( 12) hydrogen bonds : bond 0.04196 / 2.72 ( 464) hydrogen bonds : angle 4.86495 / 3.47 ( 1314) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 33 TRP cc_start: 0.7854 (t-100) cc_final: 0.7623 (t-100) REVERT: R 41 GLU cc_start: 0.8788 (tp30) cc_final: 0.8208 (tp30) REVERT: R 192 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7272 (tp) REVERT: R 262 GLU cc_start: 0.8137 (tp30) cc_final: 0.7390 (pm20) REVERT: R 289 TYR cc_start: 0.8120 (t80) cc_final: 0.7717 (t80) REVERT: R 303 MET cc_start: 0.8261 (mmt) cc_final: 0.7670 (mmt) REVERT: R 369 PHE cc_start: 0.5145 (t80) cc_final: 0.3888 (t80) REVERT: R 373 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: R 412 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7015 (tm-30) REVERT: R 418 GLU cc_start: 0.7216 (tp30) cc_final: 0.6670 (mt-10) REVERT: A 270 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8629 (mp) REVERT: B 10 GLU cc_start: 0.8602 (tm-30) cc_final: 0.7998 (tm-30) REVERT: B 12 GLU cc_start: 0.8812 (tp30) cc_final: 0.8546 (tp30) REVERT: B 211 TRP cc_start: 0.9117 (m100) cc_final: 0.8485 (m100) REVERT: B 247 ASP cc_start: 0.8419 (p0) cc_final: 0.8079 (p0) REVERT: B 254 ASP cc_start: 0.8485 (p0) cc_final: 0.8269 (p0) REVERT: B 297 TRP cc_start: 0.9077 (m100) cc_final: 0.8844 (m100) REVERT: G 48 ASP cc_start: 0.8718 (t0) cc_final: 0.8359 (t0) REVERT: N 32 TYR cc_start: 0.8238 (m-10) cc_final: 0.7963 (m-80) REVERT: N 82 GLN cc_start: 0.7439 (tp-100) cc_final: 0.7200 (tp-100) REVERT: N 98 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8575 (ptt-90) REVERT: N 105 ARG cc_start: 0.6563 (mtp-110) cc_final: 0.6206 (mtp-110) outliers start: 39 outliers final: 27 residues processed: 197 average time/residue: 0.0946 time to fit residues: 26.0829 Evaluate side-chains 190 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 371 MET Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 98 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.157685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123958 restraints weight = 12558.439| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.68 r_work: 0.3446 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9283 Z= 0.126 Angle : 0.608 12.594 12605 Z= 0.313 Chirality : 0.044 0.269 1404 Planarity : 0.004 0.065 1599 Dihedral : 4.858 34.364 1283 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.41 % Allowed : 21.30 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.25), residues: 1130 helix: 0.94 (0.25), residues: 467 sheet: -1.57 (0.33), residues: 220 loop : -1.64 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 8 TYR 0.014 0.002 TYR R 145 PHE 0.017 0.001 PHE P 28 TRP 0.055 0.002 TRP R 297 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9277) covalent geometry : angle 0.60752 / 0.31 (12593) SS BOND : bond 0.00249 / 0.14 ( 6) SS BOND : angle 0.82256 / 0.45 ( 12) hydrogen bonds : bond 0.03747 / 2.41 ( 464) hydrogen bonds : angle 4.63952 / 3.30 ( 1314) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 33 TRP cc_start: 0.7817 (t-100) cc_final: 0.7510 (t-100) REVERT: R 41 GLU cc_start: 0.8774 (tp30) cc_final: 0.8243 (tp30) REVERT: R 192 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6855 (tp) REVERT: R 262 GLU cc_start: 0.8016 (tp30) cc_final: 0.7300 (pm20) REVERT: R 289 TYR cc_start: 0.8172 (t80) cc_final: 0.7751 (t80) REVERT: R 304 ASN cc_start: 0.7557 (m-40) cc_final: 0.6174 (t0) REVERT: R 369 PHE cc_start: 0.5179 (t80) cc_final: 0.3919 (t80) REVERT: R 373 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: R 418 GLU cc_start: 0.7364 (tp30) cc_final: 0.6868 (mt-10) REVERT: A 270 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8594 (mp) REVERT: A 338 LYS cc_start: 0.8401 (ttpm) cc_final: 0.8002 (ttpp) REVERT: B 10 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8047 (tm-30) REVERT: B 12 GLU cc_start: 0.8722 (tp30) cc_final: 0.8419 (tp30) REVERT: B 211 TRP cc_start: 0.8994 (m100) cc_final: 0.8510 (m100) REVERT: B 247 ASP cc_start: 0.8395 (p0) cc_final: 0.8053 (p0) REVERT: G 48 ASP cc_start: 0.8745 (t0) cc_final: 0.8398 (t0) REVERT: N 82 GLN cc_start: 0.7286 (tp-100) cc_final: 0.6854 (tp-100) REVERT: N 98 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8636 (ptt-90) REVERT: N 105 ARG cc_start: 0.6493 (mtp-110) cc_final: 0.6199 (mtp-110) outliers start: 32 outliers final: 22 residues processed: 197 average time/residue: 0.1005 time to fit residues: 27.4986 Evaluate side-chains 194 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 98 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 26 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.159064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126075 restraints weight = 12614.540| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.58 r_work: 0.3459 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9283 Z= 0.120 Angle : 0.604 14.248 12605 Z= 0.309 Chirality : 0.043 0.273 1404 Planarity : 0.004 0.065 1599 Dihedral : 4.591 33.302 1281 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.62 % Allowed : 21.83 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.26), residues: 1130 helix: 1.09 (0.25), residues: 468 sheet: -1.31 (0.34), residues: 224 loop : -1.52 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 8 TYR 0.014 0.002 TYR R 145 PHE 0.018 0.001 PHE P 28 TRP 0.060 0.002 TRP R 297 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9277) covalent geometry : angle 0.60365 / 0.31 (12593) SS BOND : bond 0.00224 / 0.13 ( 6) SS BOND : angle 0.83393 / 0.48 ( 12) hydrogen bonds : bond 0.03636 / 2.34 ( 464) hydrogen bonds : angle 4.54656 / 3.23 ( 1314) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 33 TRP cc_start: 0.7692 (t-100) cc_final: 0.7486 (t-100) REVERT: R 262 GLU cc_start: 0.7937 (tp30) cc_final: 0.7311 (pm20) REVERT: R 304 ASN cc_start: 0.7613 (m-40) cc_final: 0.6238 (t0) REVERT: R 369 PHE cc_start: 0.5343 (t80) cc_final: 0.4119 (t80) REVERT: R 373 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: R 418 GLU cc_start: 0.7458 (tp30) cc_final: 0.7001 (mt-10) REVERT: A 270 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 338 LYS cc_start: 0.8401 (ttpm) cc_final: 0.8033 (ttpp) REVERT: B 10 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 12 GLU cc_start: 0.8696 (tp30) cc_final: 0.8394 (tp30) REVERT: B 247 ASP cc_start: 0.8376 (p0) cc_final: 0.7938 (p0) REVERT: B 304 ARG cc_start: 0.7310 (tpp80) cc_final: 0.7076 (tpp80) REVERT: G 48 ASP cc_start: 0.8714 (t0) cc_final: 0.8256 (t0) REVERT: N 72 ARG cc_start: 0.8477 (ptm160) cc_final: 0.8144 (ptm160) REVERT: N 82 GLN cc_start: 0.7180 (tp-100) cc_final: 0.6569 (tp40) REVERT: N 98 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8553 (ptt-90) REVERT: N 105 ARG cc_start: 0.6508 (mtp-110) cc_final: 0.6193 (mtp-110) outliers start: 34 outliers final: 22 residues processed: 195 average time/residue: 0.0937 time to fit residues: 25.4476 Evaluate side-chains 185 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 98 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.0870 chunk 65 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.158000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.124539 restraints weight = 12504.602| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.62 r_work: 0.3450 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9283 Z= 0.143 Angle : 0.625 14.521 12605 Z= 0.316 Chirality : 0.045 0.281 1404 Planarity : 0.004 0.059 1599 Dihedral : 4.592 33.585 1281 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.09 % Allowed : 22.36 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.26), residues: 1130 helix: 1.10 (0.25), residues: 467 sheet: -1.33 (0.34), residues: 227 loop : -1.46 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 8 TYR 0.014 0.002 TYR B 289 PHE 0.017 0.001 PHE P 28 TRP 0.068 0.002 TRP R 297 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 9277) covalent geometry : angle 0.62491 / 0.32 (12593) SS BOND : bond 0.00272 / 0.15 ( 6) SS BOND : angle 0.77734 / 0.43 ( 12) hydrogen bonds : bond 0.03686 / 2.37 ( 464) hydrogen bonds : angle 4.51953 / 3.21 ( 1314) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7167 (tp) REVERT: R 262 GLU cc_start: 0.8029 (tp30) cc_final: 0.7330 (pm20) REVERT: R 304 ASN cc_start: 0.7575 (m-40) cc_final: 0.6221 (t0) REVERT: R 369 PHE cc_start: 0.5334 (t80) cc_final: 0.4094 (t80) REVERT: R 373 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: R 412 GLU cc_start: 0.7222 (tm-30) cc_final: 0.7008 (tm-30) REVERT: A 270 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8591 (mp) REVERT: A 338 LYS cc_start: 0.8381 (ttpm) cc_final: 0.7991 (ttpp) REVERT: B 10 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8036 (tm-30) REVERT: B 12 GLU cc_start: 0.8699 (tp30) cc_final: 0.8385 (tp30) REVERT: B 211 TRP cc_start: 0.9012 (m100) cc_final: 0.8528 (m100) REVERT: B 247 ASP cc_start: 0.8372 (p0) cc_final: 0.7964 (p0) REVERT: B 304 ARG cc_start: 0.7357 (tpp80) cc_final: 0.7102 (tpp80) REVERT: G 48 ASP cc_start: 0.8763 (t0) cc_final: 0.8257 (t0) REVERT: N 72 ARG cc_start: 0.8376 (ptm160) cc_final: 0.7908 (ptm160) REVERT: N 82 GLN cc_start: 0.7252 (tp-100) cc_final: 0.6675 (tp40) REVERT: N 90 ASP cc_start: 0.8062 (m-30) cc_final: 0.7851 (m-30) REVERT: N 98 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8571 (ttp80) REVERT: N 105 ARG cc_start: 0.6625 (mtp-110) cc_final: 0.6340 (mtp-110) outliers start: 29 outliers final: 23 residues processed: 184 average time/residue: 0.0988 time to fit residues: 25.0861 Evaluate side-chains 186 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 98 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.159274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126331 restraints weight = 12388.874| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.57 r_work: 0.3457 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9283 Z= 0.135 Angle : 0.628 14.646 12605 Z= 0.317 Chirality : 0.044 0.285 1404 Planarity : 0.004 0.058 1599 Dihedral : 4.564 34.516 1281 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.19 % Allowed : 22.79 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.26), residues: 1130 helix: 1.18 (0.25), residues: 465 sheet: -1.24 (0.34), residues: 230 loop : -1.39 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 8 TYR 0.020 0.002 TYR R 289 PHE 0.017 0.001 PHE P 28 TRP 0.067 0.002 TRP R 297 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 9277) covalent geometry : angle 0.62741 / 0.32 (12593) SS BOND : bond 0.00255 / 0.14 ( 6) SS BOND : angle 0.80221 / 0.46 ( 12) hydrogen bonds : bond 0.03653 / 2.34 ( 464) hydrogen bonds : angle 4.48833 / 3.19 ( 1314) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7167 (tp) REVERT: R 262 GLU cc_start: 0.8011 (tp30) cc_final: 0.7364 (pm20) REVERT: R 303 MET cc_start: 0.8193 (mmt) cc_final: 0.7552 (mmt) REVERT: R 304 ASN cc_start: 0.7542 (m-40) cc_final: 0.6222 (t0) REVERT: R 369 PHE cc_start: 0.5394 (t80) cc_final: 0.4154 (t80) REVERT: R 373 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: R 412 GLU cc_start: 0.7232 (tm-30) cc_final: 0.7015 (tm-30) REVERT: A 270 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8561 (mp) REVERT: A 338 LYS cc_start: 0.8380 (ttpm) cc_final: 0.7990 (ttpp) REVERT: B 10 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8114 (tm-30) REVERT: B 12 GLU cc_start: 0.8681 (tp30) cc_final: 0.8336 (tp30) REVERT: B 247 ASP cc_start: 0.8382 (p0) cc_final: 0.7990 (p0) REVERT: B 280 LYS cc_start: 0.8190 (tptm) cc_final: 0.7892 (tptp) REVERT: G 48 ASP cc_start: 0.8750 (t0) cc_final: 0.8265 (t0) REVERT: N 72 ARG cc_start: 0.8291 (ptm160) cc_final: 0.7789 (ptm160) REVERT: N 74 ASN cc_start: 0.8791 (p0) cc_final: 0.8458 (p0) REVERT: N 82 GLN cc_start: 0.7155 (tp-100) cc_final: 0.6615 (tp40) REVERT: N 105 ARG cc_start: 0.6466 (mtp-110) cc_final: 0.6172 (mtp-110) outliers start: 30 outliers final: 25 residues processed: 181 average time/residue: 0.0961 time to fit residues: 24.2426 Evaluate side-chains 185 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.159607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126485 restraints weight = 12330.973| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.51 r_work: 0.3479 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9283 Z= 0.131 Angle : 0.624 14.382 12605 Z= 0.314 Chirality : 0.044 0.284 1404 Planarity : 0.004 0.058 1599 Dihedral : 4.519 33.983 1281 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.98 % Allowed : 22.90 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.26), residues: 1130 helix: 1.22 (0.25), residues: 465 sheet: -1.18 (0.34), residues: 230 loop : -1.35 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.013 0.001 TYR R 145 PHE 0.017 0.001 PHE P 28 TRP 0.064 0.002 TRP R 297 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9277) covalent geometry : angle 0.62398 / 0.31 (12593) SS BOND : bond 0.00259 / 0.15 ( 6) SS BOND : angle 0.74234 / 0.42 ( 12) hydrogen bonds : bond 0.03620 / 2.33 ( 464) hydrogen bonds : angle 4.45853 / 3.16 ( 1314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.97 seconds wall clock time: 39 minutes 16.71 seconds (2356.71 seconds total)