Starting phenix.real_space_refine on Sun May 11 13:31:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg8_37505/05_2025/8wg8_37505.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg8_37505/05_2025/8wg8_37505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wg8_37505/05_2025/8wg8_37505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg8_37505/05_2025/8wg8_37505.map" model { file = "/net/cci-nas-00/data/ceres_data/8wg8_37505/05_2025/8wg8_37505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg8_37505/05_2025/8wg8_37505.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 5114 2.51 5 N 1412 2.21 5 O 1467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8043 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1901 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2577 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 420 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2050 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 257} Chain breaks: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "E" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 13} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 5.12, per 1000 atoms: 0.64 Number of scatterers: 8043 At special positions: 0 Unit cell: (79.254, 93.177, 131.733, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1467 8.00 N 1412 7.00 C 5114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1946 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 39.8% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.587A pdb=" N LYS A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.539A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.740A pdb=" N GLU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 298 through 319 removed outlier: 4.211A pdb=" N THR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 4 through 26 removed outlier: 4.123A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.767A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.199A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.502A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.605A 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 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.657A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 165 removed outlier: 3.544A pdb=" N THR R 146 " --> pdb=" O GLN R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 202 Processing helix chain 'R' and resid 221 through 253 removed outlier: 3.614A pdb=" N VAL R 236 " --> pdb=" O GLN R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 Processing helix chain 'R' and resid 273 through 290 Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 304 through 336 removed outlier: 3.632A pdb=" N ARG R 308 " --> pdb=" O TRP R 304 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE R 309 " --> pdb=" O TRP R 305 " (cutoff:3.500A) Proline residue: R 310 - end of helix removed outlier: 3.746A pdb=" N ARG R 336 " --> pdb=" O LYS R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 355 removed outlier: 3.911A pdb=" N SER R 350 " --> pdb=" O ARG R 346 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR R 351 " --> pdb=" O LEU R 347 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 367 Processing helix chain 'R' and resid 375 through 382 Processing helix chain 'R' and resid 384 through 402 removed outlier: 3.503A pdb=" N SER R 389 " --> pdb=" O ASP R 385 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER R 390 " --> pdb=" O LEU R 386 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 419 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.663A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.779A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.583A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.042A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.835A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.220A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.834A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.762A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.878A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL N 124 " --> pdb=" O ALA N 92 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1595 1.33 - 1.45: 2032 1.45 - 1.57: 4510 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 8207 Sorted by residual: bond pdb=" CA PHE A 279 " pdb=" C PHE A 279 " ideal model delta sigma weight residual 1.523 1.565 -0.043 1.00e-02 1.00e+04 1.81e+01 bond pdb=" C PHE A 279 " pdb=" N PRO A 280 " ideal model delta sigma weight residual 1.335 1.379 -0.044 1.19e-02 7.06e+03 1.40e+01 bond pdb=" CA ARG A 309 " pdb=" C ARG A 309 " ideal model delta sigma weight residual 1.524 1.476 0.047 1.27e-02 6.20e+03 1.39e+01 bond pdb=" CA CYS N 99 " pdb=" C CYS N 99 " ideal model delta sigma weight residual 1.522 1.492 0.030 9.10e-03 1.21e+04 1.12e+01 bond pdb=" CA PHE A 223 " pdb=" C PHE A 223 " ideal model delta sigma weight residual 1.521 1.486 0.036 1.17e-02 7.31e+03 9.29e+00 ... (remaining 8202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 10888 2.00 - 3.99: 200 3.99 - 5.99: 26 5.99 - 7.98: 5 7.98 - 9.98: 3 Bond angle restraints: 11122 Sorted by residual: angle pdb=" N GLN A 52 " pdb=" CA GLN A 52 " pdb=" C GLN A 52 " ideal model delta sigma weight residual 111.40 101.42 9.98 1.22e+00 6.72e-01 6.69e+01 angle pdb=" N ARG A 54 " pdb=" CA ARG A 54 " pdb=" C ARG A 54 " ideal model delta sigma weight residual 113.88 106.43 7.45 1.23e+00 6.61e-01 3.67e+01 angle pdb=" N GLN A 24 " pdb=" CA GLN A 24 " pdb=" C GLN A 24 " ideal model delta sigma weight residual 113.12 106.03 7.09 1.25e+00 6.40e-01 3.22e+01 angle pdb=" N TYR N 115 " pdb=" CA TYR N 115 " pdb=" C TYR N 115 " ideal model delta sigma weight residual 109.24 100.38 8.86 1.63e+00 3.76e-01 2.95e+01 angle pdb=" N CYS N 99 " pdb=" CA CYS N 99 " pdb=" C CYS N 99 " ideal model delta sigma weight residual 109.48 100.09 9.39 1.75e+00 3.27e-01 2.88e+01 ... (remaining 11117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4425 17.84 - 35.67: 349 35.67 - 53.51: 69 53.51 - 71.34: 18 71.34 - 89.18: 8 Dihedral angle restraints: 4869 sinusoidal: 1864 harmonic: 3005 Sorted by residual: dihedral pdb=" CB CYS R 224 " pdb=" SG CYS R 224 " pdb=" SG CYS R 294 " pdb=" CB CYS R 294 " ideal model delta sinusoidal sigma weight residual -86.00 -172.27 86.27 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -137.80 51.80 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CA ASP B 246 " pdb=" CB ASP B 246 " pdb=" CG ASP B 246 " pdb=" OD1 ASP B 246 " ideal model delta sinusoidal sigma weight residual -30.00 -88.60 58.60 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 4866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1060 0.062 - 0.125: 172 0.125 - 0.187: 18 0.187 - 0.249: 10 0.249 - 0.312: 2 Chirality restraints: 1262 Sorted by residual: chirality pdb=" CA MET A 53 " pdb=" N MET A 53 " pdb=" C MET A 53 " pdb=" CB MET A 53 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA TYR N 117 " pdb=" N TYR N 117 " pdb=" C TYR N 117 " pdb=" CB TYR N 117 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA ASP A 310 " pdb=" N ASP A 310 " pdb=" C ASP A 310 " pdb=" CB ASP A 310 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1259 not shown) Planarity restraints: 1415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS N 99 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.96e+00 pdb=" N PRO N 100 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO N 100 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO N 100 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 306 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C TYR A 306 " -0.039 2.00e-02 2.50e+03 pdb=" O TYR A 306 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 307 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 212 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ILE A 212 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE A 212 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 213 " 0.012 2.00e-02 2.50e+03 ... (remaining 1412 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 351 2.72 - 3.26: 7968 3.26 - 3.81: 13145 3.81 - 4.35: 16159 4.35 - 4.90: 27492 Nonbonded interactions: 65115 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.170 3.040 nonbonded pdb=" OD2 ASP A 26 " pdb=" NZ LYS B 78 " model vdw 2.213 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.224 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.228 3.040 ... (remaining 65110 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.720 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.005 0.047 8210 Z= 0.308 Angle : 0.684 9.979 11128 Z= 0.429 Chirality : 0.049 0.312 1262 Planarity : 0.004 0.061 1415 Dihedral : 13.928 89.180 2914 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.13 % Allowed : 1.89 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 1017 helix: 1.37 (0.28), residues: 387 sheet: -0.27 (0.33), residues: 221 loop : -0.92 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS A 324 PHE 0.027 0.002 PHE A 189 TYR 0.021 0.001 TYR B 59 ARG 0.003 0.000 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.15298 ( 392) hydrogen bonds : angle 5.97624 ( 1113) SS BOND : bond 0.00221 ( 3) SS BOND : angle 1.10333 ( 6) covalent geometry : bond 0.00455 ( 8207) covalent geometry : angle 0.68400 (11122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: B 246 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8349 (t0) REVERT: N 17 SER cc_start: 0.8150 (m) cc_final: 0.7638 (t) REVERT: R 287 CYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7433 (t) REVERT: R 290 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6009 (tm-30) REVERT: R 293 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.6109 (pp30) REVERT: R 410 GLU cc_start: 0.8887 (tp30) cc_final: 0.8551 (tp30) outliers start: 18 outliers final: 3 residues processed: 181 average time/residue: 1.2917 time to fit residues: 246.3036 Evaluate side-chains 133 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 287 CYS Chi-restraints excluded: chain R residue 290 GLU Chi-restraints excluded: chain R residue 293 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 261 GLN A 354 HIS A 357 GLN B 44 GLN B 266 HIS N 35 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.113143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.079484 restraints weight = 13614.159| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.11 r_work: 0.2948 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 8210 Z= 0.249 Angle : 0.644 8.188 11128 Z= 0.339 Chirality : 0.044 0.147 1262 Planarity : 0.005 0.048 1415 Dihedral : 6.580 85.296 1136 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.19 % Allowed : 15.70 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 1017 helix: 1.57 (0.28), residues: 391 sheet: -0.02 (0.34), residues: 215 loop : -0.99 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 282 HIS 0.004 0.001 HIS B 62 PHE 0.019 0.002 PHE A 185 TYR 0.018 0.002 TYR R 145 ARG 0.006 0.001 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 392) hydrogen bonds : angle 4.61444 ( 1113) SS BOND : bond 0.00568 ( 3) SS BOND : angle 2.05263 ( 6) covalent geometry : bond 0.00582 ( 8207) covalent geometry : angle 0.64267 (11122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8312 (mm-30) REVERT: A 297 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7800 (pp20) REVERT: A 311 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: B 217 MET cc_start: 0.8923 (pmm) cc_final: 0.8477 (pmm) REVERT: G 21 MET cc_start: 0.7605 (mpp) cc_final: 0.7380 (mpp) REVERT: N 38 ARG cc_start: 0.8753 (mtm180) cc_final: 0.7841 (mtm180) REVERT: N 46 GLU cc_start: 0.8304 (pt0) cc_final: 0.7633 (pm20) REVERT: N 53 GLN cc_start: 0.8138 (mp10) cc_final: 0.7897 (mp10) REVERT: R 231 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7084 (ttp) REVERT: R 290 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5607 (tm-30) REVERT: R 293 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.6669 (pt0) REVERT: R 408 GLN cc_start: 0.8926 (mt0) cc_final: 0.8650 (mt0) REVERT: R 410 GLU cc_start: 0.9099 (tp30) cc_final: 0.8695 (tp30) outliers start: 27 outliers final: 13 residues processed: 145 average time/residue: 1.2371 time to fit residues: 189.9197 Evaluate side-chains 143 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 138 TYR Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 290 GLU Chi-restraints excluded: chain R residue 293 GLN Chi-restraints excluded: chain R residue 385 ASP Chi-restraints excluded: chain E residue 14 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN N 31 ASN R 177 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.115467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.083678 restraints weight = 14332.095| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.17 r_work: 0.3018 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8210 Z= 0.141 Angle : 0.561 12.001 11128 Z= 0.292 Chirality : 0.041 0.164 1262 Planarity : 0.004 0.044 1415 Dihedral : 5.839 87.953 1131 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.07 % Allowed : 18.18 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.27), residues: 1017 helix: 1.78 (0.28), residues: 392 sheet: 0.04 (0.34), residues: 210 loop : -0.98 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 282 HIS 0.003 0.001 HIS R 177 PHE 0.012 0.001 PHE A 185 TYR 0.015 0.001 TYR R 145 ARG 0.005 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 392) hydrogen bonds : angle 4.30475 ( 1113) SS BOND : bond 0.00163 ( 3) SS BOND : angle 1.29436 ( 6) covalent geometry : bond 0.00325 ( 8207) covalent geometry : angle 0.56035 (11122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8362 (mm-30) REVERT: A 188 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8589 (mtmm) REVERT: A 284 ARG cc_start: 0.8517 (ptp90) cc_final: 0.8093 (ptp90) REVERT: B 59 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: B 217 MET cc_start: 0.8907 (pmm) cc_final: 0.8441 (pmm) REVERT: G 21 MET cc_start: 0.7715 (mpp) cc_final: 0.7493 (mpp) REVERT: N 38 ARG cc_start: 0.8719 (mtm180) cc_final: 0.7898 (mtm180) REVERT: N 46 GLU cc_start: 0.8248 (pt0) cc_final: 0.7647 (pm20) REVERT: N 53 GLN cc_start: 0.8271 (mp10) cc_final: 0.8001 (mp10) REVERT: R 142 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7935 (mm110) REVERT: R 231 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6998 (ttp) REVERT: R 245 GLU cc_start: 0.8726 (tp30) cc_final: 0.8513 (tp30) REVERT: R 408 GLN cc_start: 0.8939 (mt0) cc_final: 0.8639 (mt0) REVERT: R 410 GLU cc_start: 0.9056 (tp30) cc_final: 0.8717 (tp30) outliers start: 26 outliers final: 13 residues processed: 148 average time/residue: 1.1867 time to fit residues: 185.9068 Evaluate side-chains 143 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 TYR Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 385 ASP Chi-restraints excluded: chain E residue 14 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 16 optimal weight: 0.0060 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 44 GLN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.116071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.084262 restraints weight = 14327.053| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.18 r_work: 0.3053 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8210 Z= 0.128 Angle : 0.558 12.146 11128 Z= 0.290 Chirality : 0.040 0.134 1262 Planarity : 0.003 0.043 1415 Dihedral : 4.306 44.065 1124 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.78 % Allowed : 19.01 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 1017 helix: 1.90 (0.28), residues: 392 sheet: 0.02 (0.34), residues: 209 loop : -0.94 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 282 HIS 0.002 0.001 HIS B 142 PHE 0.013 0.001 PHE A 185 TYR 0.013 0.001 TYR R 145 ARG 0.010 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 392) hydrogen bonds : angle 4.15014 ( 1113) SS BOND : bond 0.00176 ( 3) SS BOND : angle 1.11550 ( 6) covalent geometry : bond 0.00294 ( 8207) covalent geometry : angle 0.55751 (11122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8320 (mm-30) REVERT: A 188 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8590 (mtmm) REVERT: A 337 GLU cc_start: 0.7705 (pm20) cc_final: 0.7501 (pm20) REVERT: B 32 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8360 (mt0) REVERT: B 47 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8835 (t) REVERT: B 59 TYR cc_start: 0.9036 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: B 188 MET cc_start: 0.9140 (mmp) cc_final: 0.8624 (mmm) REVERT: B 217 MET cc_start: 0.8905 (pmm) cc_final: 0.8408 (pmm) REVERT: N 53 GLN cc_start: 0.8309 (mp10) cc_final: 0.7996 (mp10) REVERT: R 231 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7070 (ttp) REVERT: R 405 LYS cc_start: 0.9244 (tppt) cc_final: 0.9019 (tppt) REVERT: R 408 GLN cc_start: 0.8850 (mt0) cc_final: 0.8434 (mt0) REVERT: R 410 GLU cc_start: 0.9052 (tp30) cc_final: 0.8643 (tp30) outliers start: 32 outliers final: 13 residues processed: 157 average time/residue: 1.1114 time to fit residues: 185.6875 Evaluate side-chains 139 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 138 TYR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 385 ASP Chi-restraints excluded: chain E residue 14 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.114952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.083294 restraints weight = 14167.695| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.15 r_work: 0.3014 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8210 Z= 0.156 Angle : 0.588 11.943 11128 Z= 0.303 Chirality : 0.041 0.154 1262 Planarity : 0.003 0.051 1415 Dihedral : 4.376 46.993 1124 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.13 % Allowed : 20.07 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.27), residues: 1017 helix: 1.92 (0.28), residues: 394 sheet: 0.11 (0.34), residues: 209 loop : -0.95 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 282 HIS 0.003 0.001 HIS B 142 PHE 0.014 0.001 PHE A 185 TYR 0.019 0.001 TYR R 145 ARG 0.010 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 392) hydrogen bonds : angle 4.10969 ( 1113) SS BOND : bond 0.00165 ( 3) SS BOND : angle 1.20078 ( 6) covalent geometry : bond 0.00367 ( 8207) covalent geometry : angle 0.58762 (11122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8342 (mm-30) REVERT: A 188 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8657 (mtmm) REVERT: A 337 GLU cc_start: 0.7791 (pm20) cc_final: 0.7469 (pm20) REVERT: B 32 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8342 (mt0) REVERT: B 47 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8909 (t) REVERT: B 59 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: B 217 MET cc_start: 0.8949 (pmm) cc_final: 0.8433 (pmm) REVERT: G 21 MET cc_start: 0.7695 (mpp) cc_final: 0.7260 (mpp) REVERT: N 38 ARG cc_start: 0.8819 (mtm180) cc_final: 0.8259 (ptt90) REVERT: N 46 GLU cc_start: 0.8338 (pt0) cc_final: 0.7780 (pm20) REVERT: N 53 GLN cc_start: 0.8356 (mp10) cc_final: 0.8027 (mp10) REVERT: R 231 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7228 (mtm) REVERT: R 405 LYS cc_start: 0.9235 (tppt) cc_final: 0.8951 (tppt) REVERT: R 408 GLN cc_start: 0.8924 (mt0) cc_final: 0.8469 (mt0) REVERT: R 410 GLU cc_start: 0.8969 (tp30) cc_final: 0.8615 (tp30) outliers start: 35 outliers final: 22 residues processed: 149 average time/residue: 1.1609 time to fit residues: 183.7872 Evaluate side-chains 149 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 TYR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 357 LEU Chi-restraints excluded: chain R residue 385 ASP Chi-restraints excluded: chain E residue 14 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 52 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 0.0370 chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.116699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.085269 restraints weight = 14092.479| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.15 r_work: 0.3040 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8210 Z= 0.114 Angle : 0.574 13.297 11128 Z= 0.294 Chirality : 0.040 0.151 1262 Planarity : 0.003 0.052 1415 Dihedral : 4.229 45.037 1124 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.42 % Allowed : 21.25 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 1017 helix: 1.98 (0.28), residues: 392 sheet: 0.06 (0.34), residues: 211 loop : -0.88 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 282 HIS 0.002 0.000 HIS B 311 PHE 0.011 0.001 PHE A 185 TYR 0.015 0.001 TYR R 145 ARG 0.012 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 392) hydrogen bonds : angle 3.98255 ( 1113) SS BOND : bond 0.00183 ( 3) SS BOND : angle 0.92379 ( 6) covalent geometry : bond 0.00264 ( 8207) covalent geometry : angle 0.57407 (11122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8300 (mm-30) REVERT: A 239 ASP cc_start: 0.8812 (t0) cc_final: 0.8599 (t0) REVERT: A 311 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: B 32 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8409 (mt0) REVERT: B 47 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8908 (t) REVERT: B 59 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: B 188 MET cc_start: 0.9118 (mmp) cc_final: 0.8585 (mmm) REVERT: B 217 MET cc_start: 0.8957 (pmm) cc_final: 0.8437 (pmm) REVERT: G 21 MET cc_start: 0.7758 (mpp) cc_final: 0.7294 (mpp) REVERT: N 38 ARG cc_start: 0.8759 (mtm180) cc_final: 0.8200 (ptt90) REVERT: N 46 GLU cc_start: 0.8340 (pt0) cc_final: 0.7803 (pm20) REVERT: N 53 GLN cc_start: 0.8357 (mp10) cc_final: 0.8122 (mp10) REVERT: R 231 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7191 (mtm) REVERT: R 405 LYS cc_start: 0.9206 (tppt) cc_final: 0.8944 (tppt) REVERT: R 408 GLN cc_start: 0.8926 (mt0) cc_final: 0.8479 (mt0) REVERT: R 410 GLU cc_start: 0.8940 (tp30) cc_final: 0.8720 (tp30) outliers start: 29 outliers final: 11 residues processed: 158 average time/residue: 1.1576 time to fit residues: 194.4222 Evaluate side-chains 145 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 292 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 35 ASN B 44 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 ASN R 318 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.114161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.082529 restraints weight = 14265.347| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.15 r_work: 0.3008 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8210 Z= 0.174 Angle : 0.624 13.451 11128 Z= 0.322 Chirality : 0.042 0.177 1262 Planarity : 0.004 0.050 1415 Dihedral : 4.401 49.018 1124 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.66 % Allowed : 22.20 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 1017 helix: 2.07 (0.28), residues: 386 sheet: 0.11 (0.34), residues: 209 loop : -0.92 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP R 282 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE A 185 TYR 0.015 0.001 TYR B 264 ARG 0.012 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 392) hydrogen bonds : angle 4.06204 ( 1113) SS BOND : bond 0.00197 ( 3) SS BOND : angle 1.22472 ( 6) covalent geometry : bond 0.00411 ( 8207) covalent geometry : angle 0.62304 (11122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8423 (mm-30) REVERT: A 239 ASP cc_start: 0.8858 (t0) cc_final: 0.8639 (t0) REVERT: A 337 GLU cc_start: 0.7960 (pm20) cc_final: 0.7591 (pm20) REVERT: B 32 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8459 (mt0) REVERT: B 47 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8899 (t) REVERT: B 59 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: B 188 MET cc_start: 0.9167 (mmp) cc_final: 0.8643 (mmm) REVERT: B 217 MET cc_start: 0.8948 (pmm) cc_final: 0.8539 (pmm) REVERT: G 21 MET cc_start: 0.7796 (mpp) cc_final: 0.7581 (mpp) REVERT: N 53 GLN cc_start: 0.8365 (mp10) cc_final: 0.8128 (mp10) REVERT: R 195 ASP cc_start: 0.9251 (t0) cc_final: 0.8885 (t0) REVERT: R 231 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7216 (mtm) REVERT: R 405 LYS cc_start: 0.9222 (tppt) cc_final: 0.8908 (tppt) REVERT: R 408 GLN cc_start: 0.8955 (mt0) cc_final: 0.8520 (mt0) REVERT: R 410 GLU cc_start: 0.8946 (tp30) cc_final: 0.8737 (tp30) outliers start: 31 outliers final: 17 residues processed: 154 average time/residue: 1.1442 time to fit residues: 187.1996 Evaluate side-chains 149 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 138 TYR Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain E residue 14 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN N 84 ASN R 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.115473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.083898 restraints weight = 14363.235| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.17 r_work: 0.3023 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8210 Z= 0.138 Angle : 0.613 14.333 11128 Z= 0.313 Chirality : 0.041 0.174 1262 Planarity : 0.003 0.055 1415 Dihedral : 4.344 48.114 1124 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.95 % Allowed : 23.49 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.27), residues: 1017 helix: 2.13 (0.28), residues: 386 sheet: 0.07 (0.34), residues: 211 loop : -0.88 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 282 HIS 0.005 0.001 HIS A 197 PHE 0.014 0.001 PHE E 5 TYR 0.014 0.001 TYR R 145 ARG 0.013 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 392) hydrogen bonds : angle 3.98946 ( 1113) SS BOND : bond 0.00178 ( 3) SS BOND : angle 1.03484 ( 6) covalent geometry : bond 0.00325 ( 8207) covalent geometry : angle 0.61264 (11122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8207 (pp20) REVERT: A 20 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8292 (mm-30) REVERT: A 239 ASP cc_start: 0.8827 (t0) cc_final: 0.8614 (t0) REVERT: B 32 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8473 (mt0) REVERT: B 47 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8901 (t) REVERT: B 59 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.8059 (m-80) REVERT: B 188 MET cc_start: 0.9140 (mmp) cc_final: 0.8592 (mmm) REVERT: B 217 MET cc_start: 0.8949 (pmm) cc_final: 0.8540 (pmm) REVERT: G 21 MET cc_start: 0.7668 (tpp) cc_final: 0.7452 (mpp) REVERT: N 53 GLN cc_start: 0.8374 (mp10) cc_final: 0.8137 (mp10) REVERT: N 70 ILE cc_start: 0.8901 (tt) cc_final: 0.8557 (pp) REVERT: N 87 LYS cc_start: 0.8270 (mttm) cc_final: 0.7984 (mttm) REVERT: R 195 ASP cc_start: 0.9265 (t0) cc_final: 0.8817 (t0) REVERT: R 231 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7294 (mtm) REVERT: R 405 LYS cc_start: 0.9216 (tppt) cc_final: 0.8939 (tppt) REVERT: R 408 GLN cc_start: 0.8941 (mt0) cc_final: 0.8548 (mt0) REVERT: R 410 GLU cc_start: 0.8928 (tp30) cc_final: 0.8723 (tp30) outliers start: 25 outliers final: 17 residues processed: 145 average time/residue: 1.1924 time to fit residues: 185.0149 Evaluate side-chains 149 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 TYR Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 347 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 62 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.114180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.080420 restraints weight = 13886.944| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.17 r_work: 0.2956 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8210 Z= 0.159 Angle : 0.637 14.638 11128 Z= 0.326 Chirality : 0.042 0.178 1262 Planarity : 0.004 0.059 1415 Dihedral : 4.386 49.532 1124 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.95 % Allowed : 23.61 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.27), residues: 1017 helix: 2.13 (0.28), residues: 386 sheet: 0.15 (0.34), residues: 209 loop : -0.88 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 282 HIS 0.005 0.001 HIS A 197 PHE 0.015 0.001 PHE E 5 TYR 0.014 0.001 TYR R 145 ARG 0.014 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 392) hydrogen bonds : angle 4.02679 ( 1113) SS BOND : bond 0.00194 ( 3) SS BOND : angle 1.07516 ( 6) covalent geometry : bond 0.00378 ( 8207) covalent geometry : angle 0.63629 (11122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8207 (pp20) REVERT: A 20 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8220 (mm-30) REVERT: A 337 GLU cc_start: 0.7940 (pm20) cc_final: 0.7597 (pm20) REVERT: B 32 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8444 (mt0) REVERT: B 47 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8904 (t) REVERT: B 59 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: B 188 MET cc_start: 0.9098 (mmp) cc_final: 0.8541 (mmm) REVERT: B 217 MET cc_start: 0.8927 (pmm) cc_final: 0.8516 (pmm) REVERT: G 21 MET cc_start: 0.7633 (tpp) cc_final: 0.7194 (mpp) REVERT: N 53 GLN cc_start: 0.8327 (mp10) cc_final: 0.8101 (mp10) REVERT: N 87 LYS cc_start: 0.8178 (mttm) cc_final: 0.7900 (mttm) REVERT: R 231 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7167 (mtm) REVERT: R 405 LYS cc_start: 0.9214 (tppt) cc_final: 0.8931 (tppt) REVERT: R 408 GLN cc_start: 0.8902 (mt0) cc_final: 0.8527 (mt0) REVERT: R 410 GLU cc_start: 0.8929 (tp30) cc_final: 0.8717 (tp30) outliers start: 25 outliers final: 18 residues processed: 149 average time/residue: 1.2210 time to fit residues: 192.9308 Evaluate side-chains 146 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 138 TYR Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 347 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 91 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 0.0070 chunk 93 optimal weight: 0.3980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN N 84 ASN R 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.116708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.085259 restraints weight = 14053.334| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.15 r_work: 0.3064 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8210 Z= 0.122 Angle : 0.631 14.081 11128 Z= 0.320 Chirality : 0.041 0.244 1262 Planarity : 0.004 0.061 1415 Dihedral : 4.256 46.762 1124 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.13 % Allowed : 24.44 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 1017 helix: 2.16 (0.27), residues: 389 sheet: 0.08 (0.34), residues: 211 loop : -0.89 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 282 HIS 0.004 0.000 HIS A 197 PHE 0.017 0.001 PHE E 5 TYR 0.012 0.001 TYR R 145 ARG 0.014 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 392) hydrogen bonds : angle 3.93784 ( 1113) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.76302 ( 6) covalent geometry : bond 0.00285 ( 8207) covalent geometry : angle 0.63089 (11122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8155 (pp20) REVERT: A 20 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8229 (mm-30) REVERT: A 284 ARG cc_start: 0.8796 (mpp80) cc_final: 0.8361 (ptp90) REVERT: A 337 GLU cc_start: 0.7877 (pm20) cc_final: 0.7528 (pm20) REVERT: B 32 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8462 (mt0) REVERT: B 47 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8893 (t) REVERT: B 59 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 188 MET cc_start: 0.9022 (mmp) cc_final: 0.8454 (mmm) REVERT: B 217 MET cc_start: 0.8922 (pmm) cc_final: 0.8532 (pmm) REVERT: G 21 MET cc_start: 0.7641 (tpp) cc_final: 0.7215 (mpp) REVERT: N 53 GLN cc_start: 0.8312 (mp10) cc_final: 0.8065 (mp10) REVERT: N 70 ILE cc_start: 0.8865 (tt) cc_final: 0.8530 (pp) REVERT: N 87 LYS cc_start: 0.8211 (mttm) cc_final: 0.7937 (mttm) REVERT: R 231 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7148 (mtm) REVERT: R 405 LYS cc_start: 0.9211 (tppt) cc_final: 0.8959 (tppt) REVERT: R 408 GLN cc_start: 0.8893 (mt0) cc_final: 0.8541 (mt0) outliers start: 18 outliers final: 15 residues processed: 146 average time/residue: 1.2169 time to fit residues: 188.4691 Evaluate side-chains 153 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 138 TYR Chi-restraints excluded: chain R residue 142 GLN Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 270 ILE Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 347 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.0770 chunk 4 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN N 84 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.115605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082095 restraints weight = 13711.240| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.15 r_work: 0.3000 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 8210 Z= 0.199 Angle : 0.960 59.162 11128 Z= 0.551 Chirality : 0.042 0.294 1262 Planarity : 0.003 0.057 1415 Dihedral : 4.253 46.797 1124 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.60 % Allowed : 24.09 % Favored : 73.32 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1017 helix: 2.14 (0.27), residues: 389 sheet: 0.08 (0.34), residues: 211 loop : -0.89 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 282 HIS 0.004 0.000 HIS A 197 PHE 0.017 0.001 PHE E 5 TYR 0.030 0.001 TYR R 138 ARG 0.012 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 392) hydrogen bonds : angle 3.96674 ( 1113) SS BOND : bond 0.00210 ( 3) SS BOND : angle 0.75558 ( 6) covalent geometry : bond 0.00435 ( 8207) covalent geometry : angle 0.95975 (11122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5941.01 seconds wall clock time: 102 minutes 56.37 seconds (6176.37 seconds total)