Starting phenix.real_space_refine on Sun Jun 15 09:49:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xt8_33442/06_2025/7xt8_33442_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xt8_33442/06_2025/7xt8_33442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xt8_33442/06_2025/7xt8_33442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xt8_33442/06_2025/7xt8_33442.map" model { file = "/net/cci-nas-00/data/ceres_data/7xt8_33442/06_2025/7xt8_33442_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xt8_33442/06_2025/7xt8_33442_trim.cif" } resolution = 3.1 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= 0.007 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 63 5.16 5 C 5472 2.51 5 N 1446 2.21 5 O 1544 1.98 5 H 8287 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16812 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3928 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 2 Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5108 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1909 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4793 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Chain: "R" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 189 Unusual residues: {'CLR': 5, 'PLM': 2, 'SRO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 8.10, per 1000 atoms: 0.48 Number of scatterers: 16812 At special positions: 0 Unit cell: (97.2, 100.44, 122.04, 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) S 63 16.00 O 1544 8.00 N 1446 7.00 C 5472 6.00 H 8287 1.00 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 92 " - pdb=" SG CYS R 183 " 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: 4.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 45.7% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.501A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 251 through 254 removed outlier: 4.270A pdb=" N ASN A 254 " --> pdb=" O SER A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.783A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.434A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.514A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.607A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.593A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 112 removed outlier: 3.679A pdb=" N VAL N 110 " --> pdb=" O CYS N 107 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR N 111 " --> pdb=" O PHE N 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 46 removed outlier: 3.910A pdb=" N PHE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 51 removed outlier: 3.625A pdb=" N LYS R 51 " --> pdb=" O ARG R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 72 removed outlier: 4.200A pdb=" N PHE R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 83 Processing helix chain 'R' and resid 87 through 123 removed outlier: 4.187A pdb=" N PHE R 91 " --> pdb=" O TYR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 133 through 158 Proline residue: R 148 - end of helix removed outlier: 3.585A pdb=" N ILE R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU R 154 " --> pdb=" O PHE R 150 " (cutoff:3.500A) Proline residue: R 155 - end of helix removed outlier: 3.701A pdb=" N GLN R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 174 removed outlier: 3.982A pdb=" N PHE R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 200 Processing helix chain 'R' and resid 200 through 232 Processing helix chain 'R' and resid 254 through 284 Proline residue: R 273 - end of helix Proline residue: R 282 - end of helix Processing helix chain 'R' and resid 289 through 312 removed outlier: 3.616A pdb=" N ASN R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER R 304 " --> pdb=" O GLY R 300 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY R 305 " --> pdb=" O TYR R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix removed outlier: 3.545A pdb=" N ALA R 312 " --> pdb=" O PRO R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 328 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.633A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.580A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.916A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.649A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.480A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.670A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.830A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.547A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.315A 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: 3.831A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.523A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR N 94 " --> pdb=" O THR N 122 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1242 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: 5.88 Time building geometry restraints manager: 5.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8255 1.03 - 1.23: 37 1.23 - 1.42: 3617 1.42 - 1.62: 4999 1.62 - 1.81: 88 Bond restraints: 16996 Sorted by residual: bond pdb=" CZ2 SRO R 408 " pdb=" CH2 SRO R 408 " ideal model delta sigma weight residual 1.386 1.522 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" NE ARG R 95 " pdb=" HE ARG R 95 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C ARG R 95 " pdb=" O ARG R 95 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.15e-02 7.56e+03 1.77e+01 bond pdb=" CG SRO R 408 " pdb=" CD2 SRO R 408 " ideal model delta sigma weight residual 1.438 1.509 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C13 CLR R 401 " pdb=" C17 CLR R 401 " ideal model delta sigma weight residual 1.550 1.486 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 16991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 30347 2.09 - 4.18: 146 4.18 - 6.26: 23 6.26 - 8.35: 4 8.35 - 10.44: 1 Bond angle restraints: 30521 Sorted by residual: angle pdb=" CD1 SRO R 408 " pdb=" NE1 SRO R 408 " pdb=" CE2 SRO R 408 " ideal model delta sigma weight residual 109.10 119.54 -10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" N ARG R 95 " pdb=" CA ARG R 95 " pdb=" C ARG R 95 " ideal model delta sigma weight residual 110.97 107.50 3.47 1.09e+00 8.42e-01 1.01e+01 angle pdb=" N ARG R 95 " pdb=" CA ARG R 95 " pdb=" CB ARG R 95 " ideal model delta sigma weight residual 109.91 114.26 -4.35 1.46e+00 4.69e-01 8.87e+00 angle pdb=" CG SRO R 408 " pdb=" CD1 SRO R 408 " pdb=" NE1 SRO R 408 " ideal model delta sigma weight residual 110.16 102.18 7.98 3.00e+00 1.11e-01 7.07e+00 angle pdb=" CA ARG R 95 " pdb=" C ARG R 95 " pdb=" O ARG R 95 " ideal model delta sigma weight residual 121.00 118.38 2.62 1.05e+00 9.07e-01 6.23e+00 ... (remaining 30516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 7781 23.81 - 47.63: 381 47.63 - 71.44: 78 71.44 - 95.26: 28 95.26 - 119.07: 3 Dihedral angle restraints: 8271 sinusoidal: 4613 harmonic: 3658 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" C1 CLR R 402 " pdb=" C2 CLR R 402 " pdb=" C3 CLR R 402 " pdb=" O1 CLR R 402 " ideal model delta sinusoidal sigma weight residual 180.04 60.97 119.07 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C1 CLR R 402 " pdb=" C2 CLR R 402 " pdb=" C3 CLR R 402 " pdb=" C4 CLR R 402 " ideal model delta sinusoidal sigma weight residual 57.41 -59.54 116.95 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 8268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1185 0.065 - 0.131: 132 0.131 - 0.196: 17 0.196 - 0.261: 2 0.261 - 0.327: 5 Chirality restraints: 1341 Sorted by residual: chirality pdb=" C14 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C15 CLR R 404 " pdb=" C8 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 1338 not shown) Planarity restraints: 2485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 95 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" N THR R 96 " 0.033 2.00e-02 2.50e+03 pdb=" CA THR R 96 " -0.008 2.00e-02 2.50e+03 pdb=" H THR R 96 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 147 " 0.019 5.00e-02 4.00e+02 2.81e-02 1.26e+00 pdb=" N PRO R 148 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO R 148 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 148 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO B 236 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.015 5.00e-02 4.00e+02 ... (remaining 2482 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1055 2.20 - 2.80: 34457 2.80 - 3.40: 47347 3.40 - 4.00: 61744 4.00 - 4.60: 96078 Nonbonded interactions: 240681 Sorted by model distance: nonbonded pdb=" OE2 GLU B 10 " pdb=" HZ1 LYS G 20 " model vdw 1.602 2.450 nonbonded pdb="HD22 ASN B 119 " pdb=" O GLY B 144 " model vdw 1.623 2.450 nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.627 2.450 nonbonded pdb=" O ILE B 58 " pdb=" HG SER B 316 " model vdw 1.630 2.450 nonbonded pdb=" OD2 ASP A 229 " pdb=" H THR N 113 " model vdw 1.638 2.450 ... (remaining 240676 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: 0.500 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: 0.280 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 37.500 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 8712 Z= 0.221 Angle : 0.543 10.441 11820 Z= 0.270 Chirality : 0.046 0.327 1341 Planarity : 0.002 0.028 1469 Dihedral : 14.731 119.070 3438 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.27), residues: 1039 helix: 3.15 (0.26), residues: 417 sheet: 0.94 (0.36), residues: 212 loop : 0.48 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 298 HIS 0.002 0.001 HIS R 223 PHE 0.006 0.001 PHE B 234 TYR 0.014 0.001 TYR A 253 ARG 0.007 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.17220 ( 432) hydrogen bonds : angle 6.40660 ( 1242) SS BOND : bond 0.00114 ( 3) SS BOND : angle 0.66939 ( 6) covalent geometry : bond 0.00425 ( 8709) covalent geometry : angle 0.54258 (11814) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6465 (tp30) cc_final: 0.5774 (pt0) REVERT: B 10 GLU cc_start: 0.6906 (tt0) cc_final: 0.6651 (tp30) REVERT: B 23 LYS cc_start: 0.8179 (tptp) cc_final: 0.7895 (tppt) REVERT: B 33 ILE cc_start: 0.6872 (tt) cc_final: 0.6446 (mt) REVERT: G 48 ASP cc_start: 0.7930 (t0) cc_final: 0.7647 (t0) REVERT: N 31 ASN cc_start: 0.7751 (m-40) cc_final: 0.7512 (m-40) REVERT: N 87 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7817 (mmtp) REVERT: R 50 ARG cc_start: 0.6377 (mtp180) cc_final: 0.6011 (mtm110) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.6176 time to fit residues: 143.4699 Evaluate side-chains 154 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN R 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.141552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110264 restraints weight = 29936.910| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.00 r_work: 0.3028 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8712 Z= 0.117 Angle : 0.479 7.209 11820 Z= 0.253 Chirality : 0.040 0.161 1341 Planarity : 0.003 0.035 1469 Dihedral : 6.294 80.869 1506 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.77 % Allowed : 6.28 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.27), residues: 1039 helix: 3.18 (0.26), residues: 418 sheet: 0.69 (0.35), residues: 211 loop : 0.38 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS R 109 PHE 0.012 0.001 PHE R 275 TYR 0.010 0.001 TYR A 339 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 432) hydrogen bonds : angle 4.70576 ( 1242) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.92200 ( 6) covalent geometry : bond 0.00254 ( 8709) covalent geometry : angle 0.47908 (11814) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7520 (mm-30) REVERT: G 38 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7705 (ttm) REVERT: G 48 ASP cc_start: 0.8274 (t0) cc_final: 0.8038 (t0) REVERT: N 76 LYS cc_start: 0.7704 (mtmm) cc_final: 0.7323 (ttmt) REVERT: R 170 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6994 (mt-10) REVERT: R 171 LYS cc_start: 0.7560 (mtpp) cc_final: 0.7281 (ttmm) outliers start: 7 outliers final: 5 residues processed: 168 average time/residue: 0.5885 time to fit residues: 127.1323 Evaluate side-chains 162 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 91 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN R 226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.097888 restraints weight = 30393.938| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.96 r_work: 0.2872 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8712 Z= 0.197 Angle : 0.552 4.565 11820 Z= 0.296 Chirality : 0.042 0.148 1341 Planarity : 0.004 0.039 1469 Dihedral : 6.997 69.053 1506 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.54 % Allowed : 8.05 % Favored : 90.41 % 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: 1.76 (0.27), residues: 1039 helix: 2.63 (0.26), residues: 418 sheet: 0.16 (0.33), residues: 215 loop : 0.25 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.008 0.002 HIS A 357 PHE 0.017 0.002 PHE R 275 TYR 0.019 0.002 TYR B 59 ARG 0.004 0.001 ARG R 172 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 432) hydrogen bonds : angle 4.69408 ( 1242) SS BOND : bond 0.00206 ( 3) SS BOND : angle 1.28289 ( 6) covalent geometry : bond 0.00448 ( 8709) covalent geometry : angle 0.55130 (11814) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7580 (mm-30) REVERT: B 33 ILE cc_start: 0.7772 (tt) cc_final: 0.7554 (mt) REVERT: N 89 GLU cc_start: 0.7889 (pm20) cc_final: 0.7689 (pm20) REVERT: R 170 GLU cc_start: 0.7697 (mm-30) cc_final: 0.6981 (mt-10) REVERT: R 171 LYS cc_start: 0.7667 (mtpp) cc_final: 0.7375 (ttmm) REVERT: R 313 PHE cc_start: 0.7464 (t80) cc_final: 0.6721 (t80) REVERT: R 320 ARG cc_start: 0.7472 (ttp-170) cc_final: 0.7127 (ttt-90) outliers start: 14 outliers final: 10 residues processed: 160 average time/residue: 0.6823 time to fit residues: 140.1802 Evaluate side-chains 157 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 116 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 0.0980 chunk 93 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 120 GLN R 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.096823 restraints weight = 30508.929| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.95 r_work: 0.2862 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8712 Z= 0.175 Angle : 0.517 5.276 11820 Z= 0.275 Chirality : 0.041 0.142 1341 Planarity : 0.004 0.036 1469 Dihedral : 6.281 48.820 1506 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.32 % Allowed : 10.92 % Favored : 87.76 % 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: 1.59 (0.27), residues: 1039 helix: 2.58 (0.26), residues: 413 sheet: -0.01 (0.33), residues: 219 loop : 0.16 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS R 221 PHE 0.015 0.001 PHE R 275 TYR 0.013 0.001 TYR A 339 ARG 0.007 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 432) hydrogen bonds : angle 4.57695 ( 1242) SS BOND : bond 0.00207 ( 3) SS BOND : angle 1.19404 ( 6) covalent geometry : bond 0.00396 ( 8709) covalent geometry : angle 0.51640 (11814) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ILE cc_start: 0.7900 (tt) cc_final: 0.7620 (mt) REVERT: G 36 ASP cc_start: 0.7998 (m-30) cc_final: 0.7784 (m-30) REVERT: R 170 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7176 (mt-10) REVERT: R 171 LYS cc_start: 0.7711 (mtpp) cc_final: 0.7371 (ttmm) REVERT: R 313 PHE cc_start: 0.7480 (t80) cc_final: 0.6728 (t80) REVERT: R 320 ARG cc_start: 0.7467 (ttp-170) cc_final: 0.7136 (ttt-90) outliers start: 12 outliers final: 10 residues processed: 155 average time/residue: 0.6604 time to fit residues: 128.4325 Evaluate side-chains 155 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 116 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 58 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN R 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.096658 restraints weight = 30939.878| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.09 r_work: 0.2857 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8712 Z= 0.138 Angle : 0.487 4.416 11820 Z= 0.258 Chirality : 0.040 0.142 1341 Planarity : 0.003 0.036 1469 Dihedral : 5.840 46.264 1506 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.88 % Allowed : 12.57 % Favored : 86.55 % 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: 1.63 (0.27), residues: 1039 helix: 2.68 (0.26), residues: 413 sheet: 0.02 (0.34), residues: 210 loop : 0.07 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 221 PHE 0.013 0.001 PHE R 275 TYR 0.012 0.001 TYR A 339 ARG 0.003 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 432) hydrogen bonds : angle 4.44319 ( 1242) SS BOND : bond 0.00214 ( 3) SS BOND : angle 1.12634 ( 6) covalent geometry : bond 0.00307 ( 8709) covalent geometry : angle 0.48599 (11814) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 LEU cc_start: 0.8931 (mt) cc_final: 0.8703 (mt) REVERT: B 33 ILE cc_start: 0.7786 (tt) cc_final: 0.7532 (mt) REVERT: B 217 MET cc_start: 0.8414 (ptt) cc_final: 0.7843 (ppp) REVERT: G 22 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6392 (mt-10) REVERT: G 36 ASP cc_start: 0.7938 (m-30) cc_final: 0.7671 (m-30) REVERT: R 170 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7231 (mt-10) REVERT: R 171 LYS cc_start: 0.7682 (mtpp) cc_final: 0.7355 (ttmm) REVERT: R 313 PHE cc_start: 0.7490 (t80) cc_final: 0.7259 (t80) REVERT: R 320 ARG cc_start: 0.7447 (ttp-170) cc_final: 0.7130 (ttt-90) outliers start: 8 outliers final: 7 residues processed: 157 average time/residue: 0.6879 time to fit residues: 136.8603 Evaluate side-chains 157 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 116 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.092083 restraints weight = 31055.669| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.08 r_work: 0.2812 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8712 Z= 0.262 Angle : 0.577 5.379 11820 Z= 0.308 Chirality : 0.043 0.153 1341 Planarity : 0.004 0.040 1469 Dihedral : 7.013 52.205 1506 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.54 % Allowed : 12.90 % Favored : 85.56 % 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: 1.20 (0.26), residues: 1039 helix: 2.25 (0.26), residues: 412 sheet: -0.28 (0.34), residues: 219 loop : -0.01 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.007 0.002 HIS R 221 PHE 0.017 0.002 PHE R 275 TYR 0.017 0.002 TYR B 59 ARG 0.005 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 432) hydrogen bonds : angle 4.73409 ( 1242) SS BOND : bond 0.00309 ( 3) SS BOND : angle 1.37335 ( 6) covalent geometry : bond 0.00608 ( 8709) covalent geometry : angle 0.57654 (11814) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7394 (tp30) cc_final: 0.7191 (mm-30) REVERT: B 33 ILE cc_start: 0.7922 (tt) cc_final: 0.7678 (mt) REVERT: B 217 MET cc_start: 0.8486 (ptt) cc_final: 0.7932 (ppp) REVERT: G 22 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6583 (mt-10) REVERT: G 36 ASP cc_start: 0.7913 (m-30) cc_final: 0.7642 (m-30) REVERT: R 91 PHE cc_start: 0.7917 (t80) cc_final: 0.7557 (t80) REVERT: R 170 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7274 (mt-10) REVERT: R 171 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7596 (tttp) REVERT: R 313 PHE cc_start: 0.7591 (t80) cc_final: 0.7223 (t80) REVERT: R 320 ARG cc_start: 0.7461 (ttp-170) cc_final: 0.7130 (ttt-90) outliers start: 14 outliers final: 14 residues processed: 156 average time/residue: 0.7266 time to fit residues: 142.5484 Evaluate side-chains 159 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 116 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 80 optimal weight: 0.0170 chunk 65 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.096972 restraints weight = 30365.720| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.04 r_work: 0.2869 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8712 Z= 0.100 Angle : 0.465 4.435 11820 Z= 0.246 Chirality : 0.039 0.181 1341 Planarity : 0.004 0.049 1469 Dihedral : 5.599 48.380 1506 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.88 % Allowed : 13.45 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1039 helix: 2.69 (0.26), residues: 413 sheet: -0.08 (0.35), residues: 210 loop : -0.01 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.011 0.001 PHE R 275 TYR 0.011 0.001 TYR A 339 ARG 0.011 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 432) hydrogen bonds : angle 4.35399 ( 1242) SS BOND : bond 0.00176 ( 3) SS BOND : angle 1.03340 ( 6) covalent geometry : bond 0.00217 ( 8709) covalent geometry : angle 0.46469 (11814) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7092 (tp30) cc_final: 0.6805 (mm-30) REVERT: A 347 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7872 (ttm-80) REVERT: B 217 MET cc_start: 0.8343 (ptt) cc_final: 0.7807 (ppp) REVERT: B 219 ARG cc_start: 0.8528 (mmt90) cc_final: 0.8309 (mmt90) REVERT: G 22 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6626 (mt-10) REVERT: G 36 ASP cc_start: 0.7944 (m-30) cc_final: 0.7631 (m-30) REVERT: G 42 GLU cc_start: 0.8318 (tt0) cc_final: 0.7874 (mm-30) REVERT: R 31 MET cc_start: 0.7459 (mmp) cc_final: 0.6775 (mtt) REVERT: R 170 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7240 (mt-10) REVERT: R 171 LYS cc_start: 0.7720 (mtpp) cc_final: 0.7408 (ttmm) REVERT: R 313 PHE cc_start: 0.7563 (t80) cc_final: 0.7199 (t80) REVERT: R 320 ARG cc_start: 0.7509 (ttp-170) cc_final: 0.7195 (ttt-90) outliers start: 8 outliers final: 6 residues processed: 163 average time/residue: 0.7232 time to fit residues: 149.1549 Evaluate side-chains 159 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 132 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.095820 restraints weight = 30517.926| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.97 r_work: 0.2849 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8712 Z= 0.166 Angle : 0.503 4.512 11820 Z= 0.267 Chirality : 0.040 0.149 1341 Planarity : 0.004 0.049 1469 Dihedral : 5.954 50.923 1506 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.10 % Allowed : 13.45 % Favored : 85.45 % 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: 1.50 (0.27), residues: 1039 helix: 2.64 (0.26), residues: 413 sheet: -0.13 (0.35), residues: 210 loop : -0.03 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.004 0.001 HIS R 221 PHE 0.013 0.001 PHE R 275 TYR 0.013 0.001 TYR A 339 ARG 0.011 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 432) hydrogen bonds : angle 4.44436 ( 1242) SS BOND : bond 0.00233 ( 3) SS BOND : angle 1.24930 ( 6) covalent geometry : bond 0.00376 ( 8709) covalent geometry : angle 0.50199 (11814) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.8401 (ptt) cc_final: 0.7892 (ppp) REVERT: G 22 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6574 (mt-10) REVERT: G 36 ASP cc_start: 0.7903 (m-30) cc_final: 0.7595 (m-30) REVERT: R 154 LEU cc_start: 0.8889 (tt) cc_final: 0.8671 (tp) REVERT: R 170 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7274 (mt-10) REVERT: R 313 PHE cc_start: 0.7576 (t80) cc_final: 0.7188 (t80) REVERT: R 320 ARG cc_start: 0.7523 (ttp-170) cc_final: 0.7193 (ttt-90) outliers start: 10 outliers final: 9 residues processed: 153 average time/residue: 0.7162 time to fit residues: 135.9903 Evaluate side-chains 154 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 116 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.094742 restraints weight = 30796.057| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.09 r_work: 0.2833 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8712 Z= 0.164 Angle : 0.507 4.597 11820 Z= 0.270 Chirality : 0.040 0.139 1341 Planarity : 0.004 0.058 1469 Dihedral : 6.041 52.429 1506 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.21 % Allowed : 14.00 % Favored : 84.79 % 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: 1.43 (0.27), residues: 1039 helix: 2.55 (0.26), residues: 413 sheet: -0.16 (0.35), residues: 210 loop : -0.03 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.004 0.001 HIS R 221 PHE 0.012 0.001 PHE R 275 TYR 0.013 0.001 TYR A 339 ARG 0.011 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 432) hydrogen bonds : angle 4.45670 ( 1242) SS BOND : bond 0.00235 ( 3) SS BOND : angle 1.28101 ( 6) covalent geometry : bond 0.00370 ( 8709) covalent geometry : angle 0.50621 (11814) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.6941 (t0) cc_final: 0.6741 (t0) REVERT: A 306 SER cc_start: 0.7183 (t) cc_final: 0.6625 (p) REVERT: B 217 MET cc_start: 0.8406 (ptt) cc_final: 0.7905 (ppp) REVERT: G 22 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6511 (mt-10) REVERT: G 36 ASP cc_start: 0.7882 (m-30) cc_final: 0.7563 (m-30) REVERT: R 91 PHE cc_start: 0.7897 (t80) cc_final: 0.7627 (t80) REVERT: R 170 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7222 (mt-10) REVERT: R 313 PHE cc_start: 0.7614 (t80) cc_final: 0.7190 (t80) REVERT: R 320 ARG cc_start: 0.7526 (ttp-170) cc_final: 0.7199 (ttt-90) outliers start: 11 outliers final: 9 residues processed: 156 average time/residue: 0.7136 time to fit residues: 139.0541 Evaluate side-chains 156 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 116 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.094795 restraints weight = 30843.131| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.98 r_work: 0.2835 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8712 Z= 0.177 Angle : 0.520 4.634 11820 Z= 0.277 Chirality : 0.040 0.141 1341 Planarity : 0.004 0.058 1469 Dihedral : 6.185 52.924 1506 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.99 % Allowed : 14.33 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.27), residues: 1039 helix: 2.49 (0.26), residues: 413 sheet: -0.14 (0.35), residues: 211 loop : -0.06 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS R 221 PHE 0.013 0.001 PHE R 275 TYR 0.014 0.001 TYR A 339 ARG 0.012 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 432) hydrogen bonds : angle 4.49732 ( 1242) SS BOND : bond 0.00258 ( 3) SS BOND : angle 1.29008 ( 6) covalent geometry : bond 0.00402 ( 8709) covalent geometry : angle 0.51951 (11814) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 SER cc_start: 0.7156 (t) cc_final: 0.6599 (p) REVERT: B 217 MET cc_start: 0.8400 (ptt) cc_final: 0.7908 (ppp) REVERT: G 22 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6514 (mt-10) REVERT: G 36 ASP cc_start: 0.7854 (m-30) cc_final: 0.7538 (m-30) REVERT: N 5 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7233 (mp10) REVERT: R 91 PHE cc_start: 0.7932 (t80) cc_final: 0.7626 (t80) REVERT: R 170 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7215 (mt-10) REVERT: R 313 PHE cc_start: 0.7608 (t80) cc_final: 0.7178 (t80) REVERT: R 320 ARG cc_start: 0.7533 (ttp-170) cc_final: 0.7204 (ttt-90) outliers start: 9 outliers final: 9 residues processed: 154 average time/residue: 0.6666 time to fit residues: 129.7534 Evaluate side-chains 153 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 116 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.094193 restraints weight = 30752.741| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.10 r_work: 0.2820 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8712 Z= 0.175 Angle : 0.519 4.656 11820 Z= 0.277 Chirality : 0.041 0.170 1341 Planarity : 0.004 0.055 1469 Dihedral : 6.207 53.272 1506 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.10 % Allowed : 14.33 % Favored : 84.56 % 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: 1.32 (0.27), residues: 1039 helix: 2.46 (0.26), residues: 413 sheet: -0.19 (0.35), residues: 210 loop : -0.11 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS R 221 PHE 0.012 0.001 PHE R 275 TYR 0.014 0.001 TYR A 339 ARG 0.012 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 432) hydrogen bonds : angle 4.51279 ( 1242) SS BOND : bond 0.00255 ( 3) SS BOND : angle 1.28257 ( 6) covalent geometry : bond 0.00396 ( 8709) covalent geometry : angle 0.51830 (11814) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9529.65 seconds wall clock time: 162 minutes 56.52 seconds (9776.52 seconds total)