Starting phenix.real_space_refine on Wed Mar 4 07:16:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f9z_31501/03_2026/7f9z_31501_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f9z_31501/03_2026/7f9z_31501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f9z_31501/03_2026/7f9z_31501_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f9z_31501/03_2026/7f9z_31501_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f9z_31501/03_2026/7f9z_31501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f9z_31501/03_2026/7f9z_31501.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2189 atoms to isotropic. 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 64 5.16 5 C 6350 2.51 5 N 1715 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9982 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1877 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 64 Unusual residues: {'NH2': 1} Classifications: {'peptide': 6, 'undetermined': 1} Modifications used: {'PEPT-D': 6} Link IDs: {'CIS': 3, 'NH2_CTERM': 1, 'TRANS': 2} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2255 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain breaks: 1 Time building chain proxies: 2.57, per 1000 atoms: 0.26 Number of scatterers: 9982 At special positions: 0 Unit cell: (111.815, 114.95, 122.265, 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 64 16.00 O 1853 8.00 N 1715 7.00 C 6350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 508.7 milliseconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DHI C 1 " pdb=" CB DTR C 2 " pdb=" CB DAL C 3 " pdb=" CB DTR C 4 " pdb=" CB DPN C 5 " pdb=" CB DLY C 6 " Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 35.9% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.837A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.586A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 4.083A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.312A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.690A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.809A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.023A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.684A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.508A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 40 through 69 removed outlier: 3.618A pdb=" N ALA R 59 " --> pdb=" O VAL R 55 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL R 68 " --> pdb=" O THR R 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER R 69 " --> pdb=" O MET R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 75 removed outlier: 3.685A pdb=" N LEU R 74 " --> pdb=" O PHE R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 94 Processing helix chain 'R' and resid 95 through 100 Processing helix chain 'R' and resid 100 through 105 Processing helix chain 'R' and resid 112 through 147 Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.690A pdb=" N VAL R 155 " --> pdb=" O LYS R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 175 Processing helix chain 'R' and resid 176 through 179 Processing helix chain 'R' and resid 201 through 207 removed outlier: 3.617A pdb=" N VAL R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 241 removed outlier: 3.997A pdb=" N VAL R 212 " --> pdb=" O GLY R 208 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER R 217 " --> pdb=" O MET R 213 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE R 220 " --> pdb=" O VAL R 216 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) Proline residue: R 224 - end of helix Processing helix chain 'R' and resid 258 through 290 Proline residue: R 278 - end of helix removed outlier: 4.091A pdb=" N ARG R 283 " --> pdb=" O PHE R 279 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE R 290 " --> pdb=" O PHE R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 323 removed outlier: 4.154A pdb=" N ALA R 298 " --> pdb=" O SER R 294 " (cutoff:3.500A) Proline residue: R 320 - end of helix removed outlier: 3.565A pdb=" N TYR R 323 " --> pdb=" O ASN R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.534A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.531A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.560A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.354A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.063A 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: 6.827A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.368A 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: 6.763A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.665A 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: 6.855A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.640A 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: 3.552A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.601A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP E 73 " --> pdb=" O THR E 78 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR E 69 " --> pdb=" O GLN E 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.757A pdb=" N THR E 115 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR E 94 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.642A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.526A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.724A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.545A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 182 through 185 480 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1607 1.30 - 1.43: 2753 1.43 - 1.56: 5745 1.56 - 1.69: 2 1.69 - 1.82: 91 Bond restraints: 10198 Sorted by residual: bond pdb=" C DTR C 2 " pdb=" N DAL C 3 " ideal model delta sigma weight residual 1.329 1.509 -0.180 1.40e-02 5.10e+03 1.65e+02 bond pdb=" C DHI C 1 " pdb=" N DTR C 2 " ideal model delta sigma weight residual 1.329 1.499 -0.170 1.40e-02 5.10e+03 1.47e+02 bond pdb=" C DAL C 3 " pdb=" N DTR C 4 " ideal model delta sigma weight residual 1.329 1.480 -0.151 1.40e-02 5.10e+03 1.16e+02 bond pdb=" C DTR C 4 " pdb=" N DPN C 5 " ideal model delta sigma weight residual 1.329 1.476 -0.147 1.40e-02 5.10e+03 1.10e+02 bond pdb=" C DPN C 5 " pdb=" N DLY C 6 " ideal model delta sigma weight residual 1.329 1.474 -0.145 1.40e-02 5.10e+03 1.07e+02 ... (remaining 10193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 13631 1.93 - 3.87: 150 3.87 - 5.80: 30 5.80 - 7.74: 4 7.74 - 9.67: 3 Bond angle restraints: 13818 Sorted by residual: angle pdb=" CA DPN C 5 " pdb=" C DPN C 5 " pdb=" N DLY C 6 " ideal model delta sigma weight residual 116.20 125.87 -9.67 2.00e+00 2.50e-01 2.34e+01 angle pdb=" CA DTR C 2 " pdb=" C DTR C 2 " pdb=" N DAL C 3 " ideal model delta sigma weight residual 116.20 125.11 -8.91 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CB DHI C 1 " pdb=" CG DHI C 1 " pdb=" CD2 DHI C 1 " ideal model delta sigma weight residual 131.20 126.31 4.89 1.30e+00 5.92e-01 1.41e+01 angle pdb=" O DPN C 5 " pdb=" C DPN C 5 " pdb=" N DLY C 6 " ideal model delta sigma weight residual 123.00 117.19 5.81 1.60e+00 3.91e-01 1.32e+01 angle pdb=" O DTR C 2 " pdb=" C DTR C 2 " pdb=" N DAL C 3 " ideal model delta sigma weight residual 123.00 117.48 5.52 1.60e+00 3.91e-01 1.19e+01 ... (remaining 13813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 5482 17.63 - 35.26: 450 35.26 - 52.89: 75 52.89 - 70.52: 13 70.52 - 88.16: 7 Dihedral angle restraints: 6027 sinusoidal: 2362 harmonic: 3665 Sorted by residual: dihedral pdb=" CA LEU R 66 " pdb=" C LEU R 66 " pdb=" N VAL R 67 " pdb=" CA VAL R 67 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CB CYS R 116 " pdb=" SG CYS R 116 " pdb=" SG CYS R 198 " pdb=" CB CYS R 198 " ideal model delta sinusoidal sigma weight residual -86.00 -125.01 39.01 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 6024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1477 0.092 - 0.184: 73 0.184 - 0.277: 0 0.277 - 0.369: 1 0.369 - 0.461: 2 Chirality restraints: 1553 Sorted by residual: chirality pdb=" CA DPN C 5 " pdb=" N DPN C 5 " pdb=" C DPN C 5 " pdb=" CB DPN C 5 " both_signs ideal model delta sigma weight residual False -2.51 -2.05 -0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CA DLY C 6 " pdb=" N DLY C 6 " pdb=" C DLY C 6 " pdb=" CB DLY C 6 " both_signs ideal model delta sigma weight residual False -2.51 -2.10 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA DTR C 4 " pdb=" N DTR C 4 " pdb=" C DTR C 4 " pdb=" CB DTR C 4 " both_signs ideal model delta sigma weight residual False -2.51 -2.19 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 1550 not shown) Planarity restraints: 1753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO N 88 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 199 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO R 200 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO R 200 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 200 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 150 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO E 151 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.023 5.00e-02 4.00e+02 ... (remaining 1750 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 647 2.74 - 3.28: 10195 3.28 - 3.82: 16937 3.82 - 4.36: 19815 4.36 - 4.90: 34461 Nonbonded interactions: 82055 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.200 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.239 3.040 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP A 331 " pdb=" NH1 ARG A 333 " model vdw 2.264 3.120 nonbonded pdb=" O ILE E 138 " pdb=" OG1 THR E 238 " model vdw 2.266 3.040 ... (remaining 82050 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.460 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 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 : 0.006 0.436 10201 Z= 0.536 Angle : 0.561 9.672 13822 Z= 0.324 Chirality : 0.044 0.461 1553 Planarity : 0.004 0.050 1753 Dihedral : 13.178 88.155 3661 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.24), residues: 1244 helix: 2.03 (0.26), residues: 395 sheet: 1.14 (0.29), residues: 314 loop : 0.20 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 8 TYR 0.013 0.001 TYR A 311 PHE 0.022 0.001 PHE R 119 TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00482 (10198) covalent geometry : angle 0.56126 (13818) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.75208 ( 4) hydrogen bonds : bond 0.19522 ( 480) hydrogen bonds : angle 6.53407 ( 1323) Misc. bond : bond 0.43606 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 250 SER cc_start: 0.6231 (m) cc_final: 0.5993 (m) REVERT: A 266 LEU cc_start: 0.8007 (tp) cc_final: 0.7622 (tp) REVERT: A 272 ASP cc_start: 0.6629 (m-30) cc_final: 0.6303 (m-30) REVERT: A 289 LEU cc_start: 0.7925 (mp) cc_final: 0.7721 (mp) REVERT: B 61 MET cc_start: 0.6545 (ppp) cc_final: 0.6302 (ppp) REVERT: B 170 ASP cc_start: 0.6958 (t70) cc_final: 0.6514 (t70) REVERT: B 173 THR cc_start: 0.7586 (p) cc_final: 0.7283 (p) REVERT: B 186 ASP cc_start: 0.6212 (m-30) cc_final: 0.5849 (m-30) REVERT: B 190 LEU cc_start: 0.7915 (pp) cc_final: 0.7667 (pp) REVERT: B 311 HIS cc_start: 0.7106 (m-70) cc_final: 0.6428 (m-70) REVERT: E 172 THR cc_start: 0.8448 (p) cc_final: 0.8192 (p) REVERT: E 190 TYR cc_start: 0.7535 (p90) cc_final: 0.7333 (p90) REVERT: N 84 ASN cc_start: 0.7663 (m110) cc_final: 0.7424 (m110) REVERT: R 137 LEU cc_start: 0.7003 (mt) cc_final: 0.6723 (mt) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.0956 time to fit residues: 32.3075 Evaluate side-chains 219 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.2980 chunk 117 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 295 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.163515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.145501 restraints weight = 14192.615| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.27 r_work: 0.3761 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10201 Z= 0.117 Angle : 0.525 10.655 13822 Z= 0.277 Chirality : 0.043 0.464 1553 Planarity : 0.004 0.048 1753 Dihedral : 4.279 54.708 1393 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.20 % Allowed : 9.21 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.24), residues: 1244 helix: 2.02 (0.26), residues: 408 sheet: 0.98 (0.28), residues: 334 loop : 0.14 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 342 TYR 0.009 0.001 TYR E 190 PHE 0.019 0.001 PHE R 286 TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00251 (10198) covalent geometry : angle 0.52481 (13818) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.63308 ( 4) hydrogen bonds : bond 0.03515 ( 480) hydrogen bonds : angle 4.63319 ( 1323) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 247 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 SER cc_start: 0.6173 (m) cc_final: 0.5912 (m) REVERT: A 266 LEU cc_start: 0.8053 (tp) cc_final: 0.7678 (tp) REVERT: A 311 TYR cc_start: 0.6546 (m-80) cc_final: 0.6248 (m-80) REVERT: A 350 THR cc_start: 0.8312 (p) cc_final: 0.8101 (p) REVERT: A 374 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7562 (mtm-85) REVERT: A 381 ASP cc_start: 0.7707 (t0) cc_final: 0.7491 (t0) REVERT: B 61 MET cc_start: 0.7179 (ppp) cc_final: 0.6850 (ppp) REVERT: B 170 ASP cc_start: 0.7496 (t70) cc_final: 0.6970 (t70) REVERT: E 190 TYR cc_start: 0.7566 (p90) cc_final: 0.7216 (p90) REVERT: N 28 THR cc_start: 0.8066 (p) cc_final: 0.7846 (p) REVERT: N 83 MET cc_start: 0.7632 (mtt) cc_final: 0.7290 (mtt) REVERT: N 84 ASN cc_start: 0.7825 (m110) cc_final: 0.7603 (m110) REVERT: R 54 PHE cc_start: 0.7688 (t80) cc_final: 0.7419 (t80) outliers start: 13 outliers final: 7 residues processed: 254 average time/residue: 0.1014 time to fit residues: 35.6507 Evaluate side-chains 238 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 231 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 120 GLN Chi-restraints excluded: chain R residue 130 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 220 GLN B 239 ASN N 31 ASN R 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.152168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134274 restraints weight = 13803.165| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.10 r_work: 0.3629 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10201 Z= 0.221 Angle : 0.621 9.470 13822 Z= 0.327 Chirality : 0.047 0.465 1553 Planarity : 0.005 0.054 1753 Dihedral : 4.907 56.064 1393 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.03 % Allowed : 13.81 % Favored : 84.16 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.24), residues: 1244 helix: 1.63 (0.25), residues: 409 sheet: 0.67 (0.28), residues: 329 loop : 0.16 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 333 TYR 0.015 0.002 TYR N 95 PHE 0.023 0.002 PHE A 273 TRP 0.019 0.002 TRP E 36 HIS 0.011 0.002 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00492 (10198) covalent geometry : angle 0.62091 (13818) SS BOND : bond 0.00053 ( 2) SS BOND : angle 1.03809 ( 4) hydrogen bonds : bond 0.03963 ( 480) hydrogen bonds : angle 4.66345 ( 1323) Misc. bond : bond 0.00453 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 261 time to evaluate : 0.334 Fit side-chains REVERT: A 266 LEU cc_start: 0.8119 (tp) cc_final: 0.7849 (tp) REVERT: A 293 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7659 (mtmt) REVERT: A 343 LYS cc_start: 0.7584 (tttp) cc_final: 0.7272 (tttp) REVERT: A 370 GLU cc_start: 0.7597 (pm20) cc_final: 0.7262 (pm20) REVERT: A 374 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7716 (mtm-85) REVERT: A 381 ASP cc_start: 0.8031 (t0) cc_final: 0.7609 (t0) REVERT: B 78 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8257 (mmtm) REVERT: B 135 VAL cc_start: 0.7888 (t) cc_final: 0.7590 (p) REVERT: B 170 ASP cc_start: 0.7770 (t70) cc_final: 0.7479 (t70) REVERT: B 259 GLN cc_start: 0.8338 (pm20) cc_final: 0.7760 (pm20) REVERT: E 190 TYR cc_start: 0.8026 (p90) cc_final: 0.7572 (p90) REVERT: N 32 TYR cc_start: 0.8485 (m-80) cc_final: 0.7988 (m-80) REVERT: N 84 ASN cc_start: 0.7859 (m110) cc_final: 0.7629 (m110) REVERT: R 54 PHE cc_start: 0.7701 (t80) cc_final: 0.7419 (t80) outliers start: 22 outliers final: 18 residues processed: 271 average time/residue: 0.1070 time to fit residues: 39.6369 Evaluate side-chains 262 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 88 SER Chi-restraints excluded: chain R residue 120 GLN Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 301 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.0470 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134334 restraints weight = 14244.644| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.27 r_work: 0.3602 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10201 Z= 0.136 Angle : 0.547 8.400 13822 Z= 0.284 Chirality : 0.044 0.358 1553 Planarity : 0.004 0.050 1753 Dihedral : 4.545 43.347 1393 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.84 % Allowed : 16.76 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.24), residues: 1244 helix: 1.74 (0.26), residues: 408 sheet: 0.55 (0.28), residues: 330 loop : 0.09 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 280 TYR 0.013 0.001 TYR E 103 PHE 0.025 0.002 PHE R 279 TRP 0.014 0.001 TRP B 169 HIS 0.011 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00303 (10198) covalent geometry : angle 0.54670 (13818) SS BOND : bond 0.00164 ( 2) SS BOND : angle 0.74531 ( 4) hydrogen bonds : bond 0.03454 ( 480) hydrogen bonds : angle 4.41993 ( 1323) Misc. bond : bond 0.00121 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.401 Fit side-chains REVERT: A 266 LEU cc_start: 0.8200 (tp) cc_final: 0.7876 (tp) REVERT: A 293 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7670 (mtmt) REVERT: A 370 GLU cc_start: 0.7643 (pm20) cc_final: 0.7281 (pm20) REVERT: A 374 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7749 (mtm-85) REVERT: A 381 ASP cc_start: 0.8024 (t0) cc_final: 0.7580 (t0) REVERT: B 135 VAL cc_start: 0.7813 (t) cc_final: 0.7495 (p) REVERT: B 170 ASP cc_start: 0.7832 (t70) cc_final: 0.7511 (t70) REVERT: B 259 GLN cc_start: 0.8343 (pm20) cc_final: 0.8073 (pm20) REVERT: B 311 HIS cc_start: 0.7658 (m-70) cc_final: 0.7038 (m-70) REVERT: E 190 TYR cc_start: 0.8034 (p90) cc_final: 0.7652 (p90) REVERT: N 28 THR cc_start: 0.8524 (m) cc_final: 0.8090 (p) REVERT: N 83 MET cc_start: 0.7847 (mtt) cc_final: 0.7611 (mtp) REVERT: N 84 ASN cc_start: 0.7833 (m110) cc_final: 0.7613 (m110) REVERT: N 94 TYR cc_start: 0.8129 (m-80) cc_final: 0.7810 (m-80) REVERT: R 54 PHE cc_start: 0.7708 (t80) cc_final: 0.7454 (t80) REVERT: R 182 VAL cc_start: 0.8249 (p) cc_final: 0.7970 (t) outliers start: 20 outliers final: 14 residues processed: 261 average time/residue: 0.1053 time to fit residues: 37.7823 Evaluate side-chains 259 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 245 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 301 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.152178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134004 restraints weight = 14301.634| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.26 r_work: 0.3609 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10201 Z= 0.133 Angle : 0.535 7.730 13822 Z= 0.279 Chirality : 0.043 0.294 1553 Planarity : 0.005 0.050 1753 Dihedral : 4.430 34.259 1393 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.76 % Allowed : 16.85 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1244 helix: 1.87 (0.26), residues: 401 sheet: 0.52 (0.29), residues: 325 loop : 0.13 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 280 TYR 0.012 0.001 TYR R 313 PHE 0.026 0.002 PHE A 273 TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00301 (10198) covalent geometry : angle 0.53533 (13818) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.62459 ( 4) hydrogen bonds : bond 0.03359 ( 480) hydrogen bonds : angle 4.35310 ( 1323) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 254 time to evaluate : 0.382 Fit side-chains REVERT: A 266 LEU cc_start: 0.8165 (tp) cc_final: 0.7844 (tp) REVERT: A 370 GLU cc_start: 0.7633 (pm20) cc_final: 0.7285 (pm20) REVERT: A 374 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7496 (mtt-85) REVERT: A 381 ASP cc_start: 0.8046 (t0) cc_final: 0.7541 (t0) REVERT: B 135 VAL cc_start: 0.7791 (t) cc_final: 0.7484 (p) REVERT: B 170 ASP cc_start: 0.7823 (t70) cc_final: 0.7507 (t70) REVERT: B 219 ARG cc_start: 0.7732 (ttm110) cc_final: 0.7427 (ttm-80) REVERT: B 259 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: B 297 TRP cc_start: 0.8699 (m100) cc_final: 0.8496 (m100) REVERT: B 325 MET cc_start: 0.7728 (mmm) cc_final: 0.7238 (mmm) REVERT: E 190 TYR cc_start: 0.7994 (p90) cc_final: 0.7560 (p90) REVERT: N 28 THR cc_start: 0.8490 (m) cc_final: 0.8146 (p) REVERT: N 83 MET cc_start: 0.7889 (mtt) cc_final: 0.7665 (mtp) REVERT: N 84 ASN cc_start: 0.7811 (m110) cc_final: 0.7608 (m110) REVERT: N 94 TYR cc_start: 0.8077 (m-80) cc_final: 0.7812 (m-80) REVERT: R 54 PHE cc_start: 0.7668 (t80) cc_final: 0.7420 (t80) REVERT: R 182 VAL cc_start: 0.8238 (p) cc_final: 0.8010 (t) outliers start: 30 outliers final: 20 residues processed: 270 average time/residue: 0.1070 time to fit residues: 39.6034 Evaluate side-chains 263 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 120 GLN Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 301 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 59 optimal weight: 0.0870 chunk 17 optimal weight: 0.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 239 ASN B 311 HIS E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.149817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131892 restraints weight = 14065.737| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.11 r_work: 0.3592 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10201 Z= 0.164 Angle : 0.566 7.314 13822 Z= 0.294 Chirality : 0.044 0.287 1553 Planarity : 0.005 0.051 1753 Dihedral : 4.609 36.654 1393 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.04 % Allowed : 18.05 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1244 helix: 1.75 (0.26), residues: 401 sheet: 0.41 (0.29), residues: 325 loop : 0.11 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 280 TYR 0.013 0.002 TYR N 115 PHE 0.022 0.002 PHE R 286 TRP 0.012 0.002 TRP E 36 HIS 0.014 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00372 (10198) covalent geometry : angle 0.56583 (13818) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.63881 ( 4) hydrogen bonds : bond 0.03516 ( 480) hydrogen bonds : angle 4.43293 ( 1323) Misc. bond : bond 0.00096 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 264 time to evaluate : 0.389 Fit side-chains REVERT: A 266 LEU cc_start: 0.8179 (tp) cc_final: 0.7726 (tp) REVERT: A 270 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7905 (mp) REVERT: A 293 LYS cc_start: 0.8266 (mtpt) cc_final: 0.7628 (mtmt) REVERT: A 370 GLU cc_start: 0.7621 (pm20) cc_final: 0.7167 (pm20) REVERT: A 374 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7834 (mtm-85) REVERT: A 381 ASP cc_start: 0.8086 (t0) cc_final: 0.7566 (t0) REVERT: B 78 LYS cc_start: 0.8235 (mmtm) cc_final: 0.8028 (mmtt) REVERT: B 135 VAL cc_start: 0.7804 (t) cc_final: 0.7535 (p) REVERT: B 170 ASP cc_start: 0.7838 (t70) cc_final: 0.7559 (t70) REVERT: B 219 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7583 (ttm-80) REVERT: B 239 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7582 (t0) REVERT: B 259 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: B 297 TRP cc_start: 0.8725 (m100) cc_final: 0.8517 (m100) REVERT: B 325 MET cc_start: 0.7679 (mmm) cc_final: 0.7283 (mmm) REVERT: E 27 PHE cc_start: 0.7927 (p90) cc_final: 0.7680 (p90) REVERT: E 190 TYR cc_start: 0.8039 (p90) cc_final: 0.7599 (p90) REVERT: N 28 THR cc_start: 0.8541 (m) cc_final: 0.8195 (p) REVERT: N 34 MET cc_start: 0.7905 (mmm) cc_final: 0.7333 (mmm) REVERT: N 83 MET cc_start: 0.7812 (mtt) cc_final: 0.7601 (mtp) REVERT: N 94 TYR cc_start: 0.8151 (m-80) cc_final: 0.7788 (m-80) REVERT: R 54 PHE cc_start: 0.7588 (t80) cc_final: 0.7354 (t80) REVERT: R 182 VAL cc_start: 0.8218 (p) cc_final: 0.8002 (t) REVERT: R 213 MET cc_start: 0.4675 (pmm) cc_final: 0.3015 (ptt) outliers start: 33 outliers final: 21 residues processed: 281 average time/residue: 0.0991 time to fit residues: 38.3130 Evaluate side-chains 284 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 120 GLN Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 198 CYS Chi-restraints excluded: chain R residue 301 SER Chi-restraints excluded: chain R residue 311 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 66 optimal weight: 0.1980 chunk 88 optimal weight: 0.0870 chunk 114 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 56 optimal weight: 0.0770 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 88 ASN B 220 GLN B 239 ASN N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.152278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134394 restraints weight = 14046.180| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.11 r_work: 0.3622 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10201 Z= 0.113 Angle : 0.536 7.248 13822 Z= 0.278 Chirality : 0.043 0.273 1553 Planarity : 0.004 0.050 1753 Dihedral : 4.458 32.255 1393 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.58 % Allowed : 18.97 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.24), residues: 1244 helix: 1.83 (0.26), residues: 401 sheet: 0.59 (0.29), residues: 321 loop : 0.07 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 280 TYR 0.014 0.001 TYR R 313 PHE 0.023 0.001 PHE R 286 TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00249 (10198) covalent geometry : angle 0.53585 (13818) SS BOND : bond 0.00173 ( 2) SS BOND : angle 0.54828 ( 4) hydrogen bonds : bond 0.03287 ( 480) hydrogen bonds : angle 4.33344 ( 1323) Misc. bond : bond 0.00208 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 0.332 Fit side-chains REVERT: A 39 ARG cc_start: 0.7789 (ptp-110) cc_final: 0.7449 (ttm-80) REVERT: A 60 MET cc_start: 0.6795 (mmm) cc_final: 0.5704 (mmm) REVERT: A 222 PHE cc_start: 0.7861 (m-80) cc_final: 0.7576 (m-80) REVERT: A 266 LEU cc_start: 0.8174 (tp) cc_final: 0.7721 (tp) REVERT: A 270 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7892 (mp) REVERT: A 293 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7581 (mtmt) REVERT: A 370 GLU cc_start: 0.7678 (pm20) cc_final: 0.7302 (pm20) REVERT: A 374 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7464 (mtt-85) REVERT: A 381 ASP cc_start: 0.7965 (t0) cc_final: 0.7443 (t0) REVERT: B 135 VAL cc_start: 0.7676 (t) cc_final: 0.7417 (p) REVERT: B 170 ASP cc_start: 0.7796 (t70) cc_final: 0.7547 (t70) REVERT: B 217 MET cc_start: 0.7471 (ptm) cc_final: 0.7243 (ptm) REVERT: B 259 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: B 297 TRP cc_start: 0.8696 (m100) cc_final: 0.8474 (m100) REVERT: B 311 HIS cc_start: 0.7407 (m-70) cc_final: 0.6722 (m-70) REVERT: B 325 MET cc_start: 0.7525 (mmm) cc_final: 0.7095 (mmm) REVERT: E 27 PHE cc_start: 0.7923 (p90) cc_final: 0.7683 (p90) REVERT: E 190 TYR cc_start: 0.7996 (p90) cc_final: 0.7576 (p90) REVERT: E 223 ASP cc_start: 0.7541 (m-30) cc_final: 0.7134 (m-30) REVERT: N 28 THR cc_start: 0.8549 (m) cc_final: 0.8231 (p) REVERT: N 34 MET cc_start: 0.7925 (mmm) cc_final: 0.7370 (mmm) REVERT: R 182 VAL cc_start: 0.8223 (p) cc_final: 0.8013 (t) outliers start: 28 outliers final: 19 residues processed: 271 average time/residue: 0.1029 time to fit residues: 38.8721 Evaluate side-chains 272 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 120 GLN Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 198 CYS Chi-restraints excluded: chain R residue 301 SER Chi-restraints excluded: chain R residue 311 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 88 ASN B 220 GLN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.152286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.134317 restraints weight = 13970.071| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.12 r_work: 0.3627 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10201 Z= 0.123 Angle : 0.573 11.715 13822 Z= 0.294 Chirality : 0.043 0.278 1553 Planarity : 0.005 0.085 1753 Dihedral : 4.467 33.970 1393 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.85 % Allowed : 19.52 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.24), residues: 1244 helix: 1.81 (0.26), residues: 401 sheet: 0.66 (0.29), residues: 328 loop : 0.01 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 280 TYR 0.013 0.001 TYR R 313 PHE 0.025 0.001 PHE R 286 TRP 0.016 0.001 TRP R 109 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00273 (10198) covalent geometry : angle 0.57307 (13818) SS BOND : bond 0.00218 ( 2) SS BOND : angle 1.09423 ( 4) hydrogen bonds : bond 0.03309 ( 480) hydrogen bonds : angle 4.33433 ( 1323) Misc. bond : bond 0.00138 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 252 time to evaluate : 0.321 Fit side-chains REVERT: A 39 ARG cc_start: 0.7795 (ptp-110) cc_final: 0.7427 (ttm-80) REVERT: A 222 PHE cc_start: 0.7862 (m-80) cc_final: 0.7578 (m-80) REVERT: A 266 LEU cc_start: 0.8157 (tp) cc_final: 0.7717 (tp) REVERT: A 270 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7903 (mp) REVERT: A 293 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7570 (mtmt) REVERT: A 370 GLU cc_start: 0.7615 (pm20) cc_final: 0.7230 (pm20) REVERT: A 374 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7458 (mtt-85) REVERT: A 381 ASP cc_start: 0.7977 (t0) cc_final: 0.7406 (t0) REVERT: B 135 VAL cc_start: 0.7639 (t) cc_final: 0.7378 (p) REVERT: B 145 TYR cc_start: 0.8041 (p90) cc_final: 0.7832 (p90) REVERT: B 170 ASP cc_start: 0.7799 (t70) cc_final: 0.7521 (t70) REVERT: B 239 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7186 (t0) REVERT: B 259 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7468 (pt0) REVERT: B 297 TRP cc_start: 0.8683 (m100) cc_final: 0.8455 (m100) REVERT: B 311 HIS cc_start: 0.7450 (m-70) cc_final: 0.6767 (m-70) REVERT: B 325 MET cc_start: 0.7606 (mmm) cc_final: 0.7243 (mmm) REVERT: E 190 TYR cc_start: 0.7990 (p90) cc_final: 0.7567 (p90) REVERT: E 223 ASP cc_start: 0.7522 (m-30) cc_final: 0.7098 (m-30) REVERT: N 28 THR cc_start: 0.8575 (m) cc_final: 0.8241 (p) REVERT: N 34 MET cc_start: 0.7896 (mmm) cc_final: 0.7336 (mmm) REVERT: R 182 VAL cc_start: 0.8207 (p) cc_final: 0.7978 (t) REVERT: R 213 MET cc_start: 0.4668 (pmm) cc_final: 0.1603 (mmm) outliers start: 31 outliers final: 20 residues processed: 266 average time/residue: 0.0969 time to fit residues: 35.5705 Evaluate side-chains 274 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 120 GLN Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 198 CYS Chi-restraints excluded: chain R residue 301 SER Chi-restraints excluded: chain R residue 311 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 88 ASN B 220 GLN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.150857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132957 restraints weight = 14019.443| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.11 r_work: 0.3604 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10201 Z= 0.154 Angle : 0.581 10.611 13822 Z= 0.300 Chirality : 0.044 0.268 1553 Planarity : 0.005 0.055 1753 Dihedral : 4.562 33.524 1393 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.76 % Allowed : 19.71 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1244 helix: 1.75 (0.26), residues: 401 sheet: 0.57 (0.29), residues: 321 loop : -0.03 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 280 TYR 0.015 0.002 TYR N 115 PHE 0.025 0.002 PHE R 286 TRP 0.012 0.002 TRP B 169 HIS 0.007 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00348 (10198) covalent geometry : angle 0.58121 (13818) SS BOND : bond 0.00184 ( 2) SS BOND : angle 1.11668 ( 4) hydrogen bonds : bond 0.03448 ( 480) hydrogen bonds : angle 4.38483 ( 1323) Misc. bond : bond 0.00214 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7817 (ptp-110) cc_final: 0.7441 (ttm-80) REVERT: A 222 PHE cc_start: 0.7890 (m-80) cc_final: 0.7598 (m-80) REVERT: A 266 LEU cc_start: 0.8165 (tp) cc_final: 0.7820 (tp) REVERT: A 370 GLU cc_start: 0.7659 (pm20) cc_final: 0.7293 (pm20) REVERT: A 374 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7530 (mtt-85) REVERT: A 381 ASP cc_start: 0.8065 (t0) cc_final: 0.7507 (t0) REVERT: A 391 TYR cc_start: 0.7729 (m-10) cc_final: 0.7428 (m-10) REVERT: B 68 ARG cc_start: 0.7317 (ptm-80) cc_final: 0.7003 (ttt-90) REVERT: B 83 ASP cc_start: 0.7344 (t0) cc_final: 0.6978 (t0) REVERT: B 135 VAL cc_start: 0.7736 (t) cc_final: 0.7468 (p) REVERT: B 170 ASP cc_start: 0.7810 (t70) cc_final: 0.7521 (t70) REVERT: B 239 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7185 (t0) REVERT: B 259 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: B 297 TRP cc_start: 0.8701 (m100) cc_final: 0.8448 (m100) REVERT: B 325 MET cc_start: 0.7645 (mmm) cc_final: 0.7264 (mmm) REVERT: E 190 TYR cc_start: 0.8012 (p90) cc_final: 0.7617 (p90) REVERT: E 223 ASP cc_start: 0.7570 (m-30) cc_final: 0.7124 (m-30) REVERT: N 28 THR cc_start: 0.8600 (m) cc_final: 0.8241 (p) REVERT: N 34 MET cc_start: 0.7887 (mmm) cc_final: 0.7319 (mmm) REVERT: N 46 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7477 (mt-10) REVERT: R 182 VAL cc_start: 0.8211 (p) cc_final: 0.7988 (t) REVERT: R 210 LEU cc_start: 0.4915 (OUTLIER) cc_final: 0.3652 (pp) REVERT: R 213 MET cc_start: 0.4781 (pmm) cc_final: 0.1621 (mmm) outliers start: 30 outliers final: 23 residues processed: 278 average time/residue: 0.0967 time to fit residues: 37.5647 Evaluate side-chains 279 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 253 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 120 GLN Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 198 CYS Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 301 SER Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 97 optimal weight: 0.0050 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 88 ASN B 239 ASN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.152859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135256 restraints weight = 13736.032| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.12 r_work: 0.3647 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 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 : 0.003 0.043 10201 Z= 0.128 Angle : 0.580 10.013 13822 Z= 0.297 Chirality : 0.044 0.268 1553 Planarity : 0.005 0.047 1753 Dihedral : 4.537 32.753 1393 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.39 % Allowed : 20.26 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1244 helix: 1.76 (0.26), residues: 401 sheet: 0.55 (0.30), residues: 316 loop : -0.07 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 280 TYR 0.014 0.002 TYR N 115 PHE 0.029 0.002 PHE R 286 TRP 0.012 0.001 TRP B 169 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00289 (10198) covalent geometry : angle 0.57967 (13818) SS BOND : bond 0.00245 ( 2) SS BOND : angle 1.08942 ( 4) hydrogen bonds : bond 0.03387 ( 480) hydrogen bonds : angle 4.34051 ( 1323) Misc. bond : bond 0.00212 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7788 (ptp-110) cc_final: 0.7414 (ttm-80) REVERT: A 60 MET cc_start: 0.7023 (mmm) cc_final: 0.5858 (mmm) REVERT: A 222 PHE cc_start: 0.7943 (m-80) cc_final: 0.7634 (m-80) REVERT: A 266 LEU cc_start: 0.8065 (tp) cc_final: 0.7772 (tp) REVERT: A 293 LYS cc_start: 0.8063 (mtpt) cc_final: 0.7498 (mtmt) REVERT: A 370 GLU cc_start: 0.7634 (pm20) cc_final: 0.7199 (pm20) REVERT: A 374 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7456 (mtt-85) REVERT: A 381 ASP cc_start: 0.8053 (t0) cc_final: 0.7462 (t0) REVERT: B 68 ARG cc_start: 0.7328 (ptm-80) cc_final: 0.6998 (ttt-90) REVERT: B 83 ASP cc_start: 0.7460 (t0) cc_final: 0.7185 (t0) REVERT: B 135 VAL cc_start: 0.7684 (t) cc_final: 0.7405 (p) REVERT: B 170 ASP cc_start: 0.7862 (t70) cc_final: 0.7507 (t70) REVERT: B 220 GLN cc_start: 0.8091 (mt0) cc_final: 0.7887 (mt0) REVERT: B 239 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.6796 (t0) REVERT: B 259 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7488 (pt0) REVERT: B 297 TRP cc_start: 0.8665 (m100) cc_final: 0.8408 (m100) REVERT: B 325 MET cc_start: 0.7678 (mmm) cc_final: 0.7403 (mmm) REVERT: E 190 TYR cc_start: 0.7954 (p90) cc_final: 0.7500 (p90) REVERT: E 223 ASP cc_start: 0.7510 (m-30) cc_final: 0.7056 (m-30) REVERT: N 28 THR cc_start: 0.8588 (m) cc_final: 0.8199 (p) REVERT: N 34 MET cc_start: 0.7916 (mmm) cc_final: 0.7369 (mmm) REVERT: N 46 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7503 (mt-10) REVERT: R 182 VAL cc_start: 0.8248 (p) cc_final: 0.8022 (t) REVERT: R 210 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.3642 (pp) REVERT: R 213 MET cc_start: 0.4740 (pmm) cc_final: 0.1575 (mmm) outliers start: 26 outliers final: 23 residues processed: 274 average time/residue: 0.0984 time to fit residues: 37.1941 Evaluate side-chains 284 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 120 GLN Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 198 CYS Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 301 SER Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 119 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 84 optimal weight: 0.0270 chunk 9 optimal weight: 1.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 44 GLN B 88 ASN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.152350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.134834 restraints weight = 13896.659| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.13 r_work: 0.3642 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10201 Z= 0.148 Angle : 0.584 9.702 13822 Z= 0.301 Chirality : 0.044 0.262 1553 Planarity : 0.005 0.057 1753 Dihedral : 4.578 32.329 1393 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.58 % Allowed : 20.53 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.24), residues: 1244 helix: 1.74 (0.26), residues: 401 sheet: 0.44 (0.29), residues: 324 loop : -0.06 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 219 TYR 0.016 0.002 TYR N 115 PHE 0.031 0.002 PHE R 286 TRP 0.012 0.001 TRP A 234 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00336 (10198) covalent geometry : angle 0.58357 (13818) SS BOND : bond 0.00193 ( 2) SS BOND : angle 1.11371 ( 4) hydrogen bonds : bond 0.03435 ( 480) hydrogen bonds : angle 4.37658 ( 1323) Misc. bond : bond 0.00201 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.65 seconds wall clock time: 46 minutes 39.36 seconds (2799.36 seconds total)