Starting phenix.real_space_refine on Sun May 11 17:09:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d4z_46571/05_2025/9d4z_46571.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d4z_46571/05_2025/9d4z_46571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d4z_46571/05_2025/9d4z_46571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d4z_46571/05_2025/9d4z_46571.map" model { file = "/net/cci-nas-00/data/ceres_data/9d4z_46571/05_2025/9d4z_46571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d4z_46571/05_2025/9d4z_46571.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5296 2.51 5 N 1371 2.21 5 O 1547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8267 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2300 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 297} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 174 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 3, 'TRANS': 20} Chain: "R" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2327 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 10, 'TRANS': 286} Chain breaks: 1 Chain: "E" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1765 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1701 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 206} Chain breaks: 3 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 4.77, per 1000 atoms: 0.58 Number of scatterers: 8267 At special positions: 0 Unit cell: (85.905, 119.025, 130.41, 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 53 16.00 O 1547 8.00 N 1371 7.00 C 5296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 175 " - pdb=" SG CYS R 254 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1996 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 39.2% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.922A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 89 through 97 Processing helix chain 'R' and resid 98 through 130 removed outlier: 4.748A pdb=" N VAL R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Proline residue: R 106 - end of helix Proline residue: R 118 - end of helix Processing helix chain 'R' and resid 135 through 154 removed outlier: 3.506A pdb=" N VAL R 139 " --> pdb=" O LYS R 135 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL R 154 " --> pdb=" O LEU R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 164 removed outlier: 3.913A pdb=" N LYS R 158 " --> pdb=" O VAL R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 206 removed outlier: 3.976A pdb=" N ARG R 176 " --> pdb=" O SER R 172 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE R 177 " --> pdb=" O GLU R 173 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET R 186 " --> pdb=" O PHE R 182 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR R 187 " --> pdb=" O TYR R 183 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE R 190 " --> pdb=" O MET R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 214 removed outlier: 3.821A pdb=" N LEU R 211 " --> pdb=" O PRO R 207 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N SER R 212 " --> pdb=" O MET R 208 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP R 213 " --> pdb=" O GLN R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 234 removed outlier: 3.555A pdb=" N VAL R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 240 removed outlier: 3.701A pdb=" N LYS R 240 " --> pdb=" O PRO R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 265 Processing helix chain 'R' and resid 265 through 279 Processing helix chain 'R' and resid 279 through 299 Processing helix chain 'R' and resid 299 through 304 removed outlier: 4.053A pdb=" N ASN R 304 " --> pdb=" O SER R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 339 Proline residue: R 328 - end of helix removed outlier: 3.619A pdb=" N PHE R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 360 removed outlier: 3.818A pdb=" N GLU R 347 " --> pdb=" O THR R 343 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA R 348 " --> pdb=" O SER R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 372 Proline residue: R 368 - end of helix Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.227A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'A' and resid 7 through 38 removed outlier: 3.656A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.669A pdb=" N PHE A 55 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 removed outlier: 3.840A pdb=" N GLN A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 250 removed outlier: 3.571A pdb=" N GLN A 239 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU A 240 " --> pdb=" O ASN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.833A pdb=" N ARG A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 279 through 284 removed outlier: 4.141A pdb=" N TYR A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 303 through 325 removed outlier: 3.728A pdb=" N PHE A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 363 removed outlier: 3.681A pdb=" N ILE A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.778A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.388A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.698A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.823A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.763A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.521A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.028A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 43 through 45 removed outlier: 5.683A pdb=" N PHE R 43 " --> pdb=" O LEU R 258 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'R' and resid 244 through 245 Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.537A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.791A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 4.054A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 189 through 191 Processing sheet with id=AB6, first strand: chain 'A' and resid 189 through 191 removed outlier: 5.007A pdb=" N VAL A 206 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY A 46 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS A 41 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE A 227 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A 43 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL A 229 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 45 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ASP A 231 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 226 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE A 262 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N PHE A 228 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 264 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 230 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL A 259 " --> pdb=" O TYR A 332 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2626 1.34 - 1.46: 2186 1.46 - 1.58: 3567 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 8455 Sorted by residual: bond pdb=" N ASP B 38 " pdb=" CA ASP B 38 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N SER R 42 " pdb=" CA SER R 42 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N ALA G 34 " pdb=" CA ALA G 34 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N SER A 6 " pdb=" CA SER A 6 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.64e+00 ... (remaining 8450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 11168 1.50 - 3.00: 259 3.00 - 4.49: 49 4.49 - 5.99: 8 5.99 - 7.49: 3 Bond angle restraints: 11487 Sorted by residual: angle pdb=" CB ARG A 38 " pdb=" CG ARG A 38 " pdb=" CD ARG A 38 " ideal model delta sigma weight residual 111.30 117.39 -6.09 2.30e+00 1.89e-01 7.01e+00 angle pdb=" CG ARG A 38 " pdb=" CD ARG A 38 " pdb=" NE ARG A 38 " ideal model delta sigma weight residual 112.00 117.74 -5.74 2.20e+00 2.07e-01 6.82e+00 angle pdb=" CB GLU B 172 " pdb=" CG GLU B 172 " pdb=" CD GLU B 172 " ideal model delta sigma weight residual 112.60 116.87 -4.27 1.70e+00 3.46e-01 6.31e+00 angle pdb=" CB ILE A 330 " pdb=" CG1 ILE A 330 " pdb=" CD1 ILE A 330 " ideal model delta sigma weight residual 113.80 119.01 -5.21 2.10e+00 2.27e-01 6.16e+00 angle pdb=" CA ILE A 330 " pdb=" CB ILE A 330 " pdb=" CG1 ILE A 330 " ideal model delta sigma weight residual 110.40 114.30 -3.90 1.70e+00 3.46e-01 5.26e+00 ... (remaining 11482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4453 17.86 - 35.73: 385 35.73 - 53.59: 97 53.59 - 71.45: 15 71.45 - 89.31: 3 Dihedral angle restraints: 4953 sinusoidal: 1851 harmonic: 3102 Sorted by residual: dihedral pdb=" CA ASP B 153 " pdb=" C ASP B 153 " pdb=" N ASP B 154 " pdb=" CA ASP B 154 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 61.14 31.86 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 64.14 28.86 1 1.00e+01 1.00e-02 1.19e+01 ... (remaining 4950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1025 0.047 - 0.095: 221 0.095 - 0.142: 65 0.142 - 0.190: 1 0.190 - 0.237: 1 Chirality restraints: 1313 Sorted by residual: chirality pdb=" CB VAL R 291 " pdb=" CA VAL R 291 " pdb=" CG1 VAL R 291 " pdb=" CG2 VAL R 291 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CG LEU R 354 " pdb=" CB LEU R 354 " pdb=" CD1 LEU R 354 " pdb=" CD2 LEU R 354 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 1310 not shown) Planarity restraints: 1444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 281 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO R 282 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 282 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 282 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER R 315 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C SER R 315 " -0.031 2.00e-02 2.50e+03 pdb=" O SER R 315 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA R 316 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP R 367 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO R 368 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO R 368 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 368 " -0.024 5.00e-02 4.00e+02 ... (remaining 1441 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 699 2.74 - 3.28: 8642 3.28 - 3.82: 13621 3.82 - 4.36: 16989 4.36 - 4.90: 29009 Nonbonded interactions: 68960 Sorted by model distance: nonbonded pdb=" NE1 TRP R 168 " pdb=" O GLY R 171 " model vdw 2.197 3.120 nonbonded pdb=" OE2 GLU A 28 " pdb=" NH2 ARG A 38 " model vdw 2.350 3.120 nonbonded pdb=" O THR B 263 " pdb=" OG1 THR B 263 " model vdw 2.371 3.040 nonbonded pdb=" O ALA B 302 " pdb=" OD1 ASP B 303 " model vdw 2.376 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.404 3.040 ... (remaining 68955 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 20.880 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:10.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8458 Z= 0.177 Angle : 0.586 7.491 11493 Z= 0.313 Chirality : 0.042 0.237 1313 Planarity : 0.004 0.050 1444 Dihedral : 14.509 89.315 2948 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 18.57 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1047 helix: 0.45 (0.29), residues: 326 sheet: -0.31 (0.30), residues: 286 loop : -0.34 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 168 HIS 0.009 0.002 HIS R 336 PHE 0.019 0.002 PHE R 274 TYR 0.016 0.002 TYR A 235 ARG 0.007 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.18439 ( 395) hydrogen bonds : angle 7.83631 ( 1104) SS BOND : bond 0.00690 ( 3) SS BOND : angle 1.52231 ( 6) covalent geometry : bond 0.00390 ( 8455) covalent geometry : angle 0.58472 (11487) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.926 Fit side-chains REVERT: B 55 LEU cc_start: 0.8395 (mt) cc_final: 0.8120 (mp) REVERT: B 72 SER cc_start: 0.8022 (t) cc_final: 0.7774 (p) REVERT: B 96 ARG cc_start: 0.7625 (mtm110) cc_final: 0.7338 (mtm110) REVERT: B 190 LEU cc_start: 0.7660 (tp) cc_final: 0.7422 (tp) REVERT: B 334 SER cc_start: 0.7720 (m) cc_final: 0.7221 (t) REVERT: E 172 THR cc_start: 0.8132 (m) cc_final: 0.7733 (p) REVERT: E 230 MET cc_start: 0.7097 (ptm) cc_final: 0.6599 (ptt) REVERT: A 52 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8116 (mtmt) REVERT: A 280 ILE cc_start: 0.8539 (mt) cc_final: 0.8332 (mp) REVERT: A 345 ARG cc_start: 0.7904 (mmm160) cc_final: 0.7133 (tpt170) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.9711 time to fit residues: 245.2815 Evaluate side-chains 226 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 88 ASN B 110 ASN B 125 ASN B 220 GLN R 255 HIS E 82 GLN E 171 ASN E 186 GLN A 200 ASN A 250 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.148649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.134248 restraints weight = 11983.137| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.03 r_work: 0.3773 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8458 Z= 0.159 Angle : 0.596 10.912 11493 Z= 0.315 Chirality : 0.044 0.168 1313 Planarity : 0.005 0.042 1444 Dihedral : 4.790 26.194 1158 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.13 % Allowed : 15.77 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1047 helix: 1.20 (0.29), residues: 329 sheet: 0.01 (0.31), residues: 277 loop : -0.33 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.007 0.002 HIS E 35 PHE 0.020 0.002 PHE R 274 TYR 0.018 0.002 TYR E 190 ARG 0.008 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 395) hydrogen bonds : angle 5.29452 ( 1104) SS BOND : bond 0.00763 ( 3) SS BOND : angle 1.52485 ( 6) covalent geometry : bond 0.00359 ( 8455) covalent geometry : angle 0.59538 (11487) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.841 Fit side-chains REVERT: B 49 ARG cc_start: 0.8263 (mmt-90) cc_final: 0.8038 (mpt180) REVERT: B 72 SER cc_start: 0.8023 (t) cc_final: 0.7760 (p) REVERT: B 75 GLN cc_start: 0.7545 (mt0) cc_final: 0.7315 (mt0) REVERT: B 119 ASN cc_start: 0.8022 (m-40) cc_final: 0.7773 (m-40) REVERT: B 273 ILE cc_start: 0.7640 (mt) cc_final: 0.7306 (mt) REVERT: B 334 SER cc_start: 0.7381 (m) cc_final: 0.6844 (t) REVERT: R 109 TYR cc_start: 0.7186 (m-80) cc_final: 0.6942 (m-80) REVERT: R 140 TYR cc_start: 0.8019 (m-80) cc_final: 0.7775 (m-80) REVERT: E 140 MET cc_start: 0.7262 (mmt) cc_final: 0.6737 (mmt) REVERT: A 17 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7861 (mtpp) REVERT: A 251 ASN cc_start: 0.8558 (t0) cc_final: 0.8330 (t160) outliers start: 28 outliers final: 13 residues processed: 230 average time/residue: 0.9996 time to fit residues: 246.8171 Evaluate side-chains 219 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 110 ASN B 125 ASN B 237 ASN E 82 GLN E 186 GLN A 200 ASN A 250 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.148565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.134080 restraints weight = 12277.428| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.07 r_work: 0.3773 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8458 Z= 0.150 Angle : 0.566 12.658 11493 Z= 0.295 Chirality : 0.042 0.177 1313 Planarity : 0.004 0.035 1444 Dihedral : 4.611 26.306 1158 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.91 % Allowed : 16.78 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1047 helix: 1.45 (0.29), residues: 329 sheet: 0.15 (0.31), residues: 272 loop : -0.30 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.005 0.001 HIS R 143 PHE 0.019 0.002 PHE R 274 TYR 0.014 0.001 TYR E 190 ARG 0.009 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 395) hydrogen bonds : angle 4.96629 ( 1104) SS BOND : bond 0.00781 ( 3) SS BOND : angle 1.38095 ( 6) covalent geometry : bond 0.00339 ( 8455) covalent geometry : angle 0.56534 (11487) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 1.133 Fit side-chains REVERT: B 61 MET cc_start: 0.8533 (ppp) cc_final: 0.8316 (ppp) REVERT: B 72 SER cc_start: 0.8041 (t) cc_final: 0.7746 (p) REVERT: B 75 GLN cc_start: 0.7556 (mt0) cc_final: 0.7293 (mt0) REVERT: B 137 ARG cc_start: 0.7435 (tpp-160) cc_final: 0.7186 (ttm-80) REVERT: B 273 ILE cc_start: 0.7677 (mt) cc_final: 0.7374 (mt) REVERT: B 334 SER cc_start: 0.7327 (m) cc_final: 0.6798 (t) REVERT: R 140 TYR cc_start: 0.8084 (m-80) cc_final: 0.7733 (m-80) REVERT: E 140 MET cc_start: 0.7393 (mmt) cc_final: 0.6815 (mmt) outliers start: 35 outliers final: 16 residues processed: 221 average time/residue: 1.0345 time to fit residues: 244.6712 Evaluate side-chains 217 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain R residue 210 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 72 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN E 186 GLN A 250 ASN A 364 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.147358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.132912 restraints weight = 12122.479| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.05 r_work: 0.3757 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8458 Z= 0.183 Angle : 0.571 8.787 11493 Z= 0.298 Chirality : 0.043 0.182 1313 Planarity : 0.004 0.039 1444 Dihedral : 4.647 27.370 1158 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.47 % Allowed : 18.68 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1047 helix: 1.50 (0.29), residues: 324 sheet: 0.14 (0.30), residues: 269 loop : -0.42 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.007 0.001 HIS E 35 PHE 0.018 0.002 PHE R 274 TYR 0.022 0.002 TYR R 266 ARG 0.010 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 395) hydrogen bonds : angle 4.92870 ( 1104) SS BOND : bond 0.00868 ( 3) SS BOND : angle 1.60663 ( 6) covalent geometry : bond 0.00419 ( 8455) covalent geometry : angle 0.57013 (11487) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: B 72 SER cc_start: 0.8042 (t) cc_final: 0.7728 (p) REVERT: B 119 ASN cc_start: 0.8076 (m-40) cc_final: 0.7812 (m-40) REVERT: B 137 ARG cc_start: 0.7442 (tpp-160) cc_final: 0.7131 (ttm-80) REVERT: B 212 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7210 (m-30) REVERT: B 234 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6049 (t80) REVERT: B 314 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7205 (ttt90) REVERT: B 334 SER cc_start: 0.7367 (m) cc_final: 0.6852 (t) REVERT: R 140 TYR cc_start: 0.8097 (m-80) cc_final: 0.7700 (m-80) REVERT: E 116 THR cc_start: 0.8609 (t) cc_final: 0.8390 (p) REVERT: E 140 MET cc_start: 0.7425 (mmt) cc_final: 0.6814 (mmt) outliers start: 31 outliers final: 17 residues processed: 229 average time/residue: 0.9944 time to fit residues: 244.1428 Evaluate side-chains 222 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain R residue 210 SER Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 92 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN E 82 GLN E 186 GLN A 221 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.148316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.134072 restraints weight = 12040.328| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.03 r_work: 0.3766 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8458 Z= 0.167 Angle : 0.573 7.830 11493 Z= 0.298 Chirality : 0.043 0.197 1313 Planarity : 0.004 0.068 1444 Dihedral : 4.624 27.169 1158 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.91 % Allowed : 20.58 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1047 helix: 1.50 (0.29), residues: 325 sheet: 0.15 (0.30), residues: 266 loop : -0.42 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.006 0.001 HIS E 35 PHE 0.016 0.001 PHE R 274 TYR 0.015 0.002 TYR R 266 ARG 0.015 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 395) hydrogen bonds : angle 4.86639 ( 1104) SS BOND : bond 0.00874 ( 3) SS BOND : angle 1.56264 ( 6) covalent geometry : bond 0.00384 ( 8455) covalent geometry : angle 0.57185 (11487) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 1.041 Fit side-chains REVERT: B 72 SER cc_start: 0.8055 (t) cc_final: 0.7722 (p) REVERT: B 75 GLN cc_start: 0.7468 (mt0) cc_final: 0.7247 (mt0) REVERT: B 119 ASN cc_start: 0.8075 (m-40) cc_final: 0.7804 (m-40) REVERT: B 212 ASP cc_start: 0.7586 (m-30) cc_final: 0.7060 (m-30) REVERT: B 334 SER cc_start: 0.7370 (m) cc_final: 0.6846 (t) REVERT: R 109 TYR cc_start: 0.6812 (m-80) cc_final: 0.6608 (m-80) REVERT: R 140 TYR cc_start: 0.8079 (m-80) cc_final: 0.7670 (m-80) REVERT: E 116 THR cc_start: 0.8585 (t) cc_final: 0.8384 (p) REVERT: E 140 MET cc_start: 0.7455 (mmt) cc_final: 0.6880 (mmt) REVERT: E 192 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7267 (mmp) REVERT: A 41 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8095 (mtmm) outliers start: 35 outliers final: 20 residues processed: 224 average time/residue: 0.9854 time to fit residues: 236.7249 Evaluate side-chains 221 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 210 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.0470 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN E 186 GLN E 194 ASN A 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.148252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.134052 restraints weight = 12088.091| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.03 r_work: 0.3765 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8458 Z= 0.171 Angle : 0.575 8.664 11493 Z= 0.298 Chirality : 0.043 0.204 1313 Planarity : 0.004 0.049 1444 Dihedral : 4.616 27.423 1158 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.36 % Allowed : 20.81 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1047 helix: 1.54 (0.29), residues: 324 sheet: 0.17 (0.30), residues: 266 loop : -0.40 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.006 0.001 HIS E 35 PHE 0.016 0.002 PHE R 271 TYR 0.014 0.002 TYR E 102 ARG 0.009 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 395) hydrogen bonds : angle 4.86768 ( 1104) SS BOND : bond 0.00873 ( 3) SS BOND : angle 1.51235 ( 6) covalent geometry : bond 0.00394 ( 8455) covalent geometry : angle 0.57426 (11487) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.8464 (ppp) cc_final: 0.7656 (ppp) REVERT: B 72 SER cc_start: 0.8038 (t) cc_final: 0.7704 (p) REVERT: B 111 TYR cc_start: 0.8557 (m-80) cc_final: 0.8356 (m-80) REVERT: B 119 ASN cc_start: 0.8040 (m-40) cc_final: 0.7799 (m-40) REVERT: B 169 TRP cc_start: 0.8466 (OUTLIER) cc_final: 0.8143 (m-10) REVERT: B 217 MET cc_start: 0.7173 (mmt) cc_final: 0.6931 (mmt) REVERT: B 334 SER cc_start: 0.7476 (m) cc_final: 0.6957 (t) REVERT: R 109 TYR cc_start: 0.6831 (m-80) cc_final: 0.6577 (m-80) REVERT: R 140 TYR cc_start: 0.8070 (m-80) cc_final: 0.7692 (m-80) REVERT: R 196 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7553 (mt) REVERT: E 109 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: E 172 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7881 (p) REVERT: E 192 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7260 (mmp) REVERT: A 17 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7944 (mtpp) outliers start: 39 outliers final: 24 residues processed: 227 average time/residue: 0.9339 time to fit residues: 227.9776 Evaluate side-chains 228 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 210 SER Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 103 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN E 82 GLN E 186 GLN E 194 ASN A 200 ASN A 221 ASN A 250 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.148635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.134521 restraints weight = 12211.943| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.04 r_work: 0.3770 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8458 Z= 0.151 Angle : 0.570 7.948 11493 Z= 0.295 Chirality : 0.043 0.209 1313 Planarity : 0.004 0.038 1444 Dihedral : 4.565 27.284 1158 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.14 % Allowed : 21.48 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1047 helix: 1.59 (0.29), residues: 325 sheet: 0.18 (0.31), residues: 253 loop : -0.43 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 PHE 0.013 0.001 PHE R 274 TYR 0.013 0.001 TYR E 102 ARG 0.008 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 395) hydrogen bonds : angle 4.86919 ( 1104) SS BOND : bond 0.00776 ( 3) SS BOND : angle 1.22033 ( 6) covalent geometry : bond 0.00346 ( 8455) covalent geometry : angle 0.56948 (11487) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.898 Fit side-chains REVERT: B 61 MET cc_start: 0.8428 (ppp) cc_final: 0.7514 (ppp) REVERT: B 72 SER cc_start: 0.8031 (t) cc_final: 0.7708 (p) REVERT: B 111 TYR cc_start: 0.8563 (m-80) cc_final: 0.8354 (m-80) REVERT: B 119 ASN cc_start: 0.8038 (m-40) cc_final: 0.7780 (m-40) REVERT: B 169 TRP cc_start: 0.8462 (OUTLIER) cc_final: 0.8110 (m-10) REVERT: B 217 MET cc_start: 0.7208 (mmt) cc_final: 0.6956 (mmt) REVERT: B 334 SER cc_start: 0.7428 (m) cc_final: 0.6912 (t) REVERT: R 109 TYR cc_start: 0.6931 (m-80) cc_final: 0.6582 (m-80) REVERT: R 140 TYR cc_start: 0.8073 (m-80) cc_final: 0.7735 (m-80) REVERT: R 168 TRP cc_start: 0.6303 (t-100) cc_final: 0.5372 (t-100) REVERT: R 196 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7528 (mt) REVERT: E 18 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7803 (ptm160) REVERT: E 172 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7885 (p) REVERT: E 192 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7296 (mmp) REVERT: A 17 LYS cc_start: 0.8205 (mtpp) cc_final: 0.7988 (mtpp) outliers start: 37 outliers final: 25 residues processed: 226 average time/residue: 1.0217 time to fit residues: 247.2199 Evaluate side-chains 231 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 210 SER Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 323 ILE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 102 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 194 ASN A 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.148905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.134744 restraints weight = 12284.981| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.06 r_work: 0.3770 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8458 Z= 0.149 Angle : 0.572 7.946 11493 Z= 0.295 Chirality : 0.043 0.216 1313 Planarity : 0.004 0.052 1444 Dihedral : 4.534 27.233 1158 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.80 % Allowed : 22.71 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1047 helix: 1.59 (0.29), residues: 326 sheet: 0.14 (0.31), residues: 261 loop : -0.39 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 PHE 0.020 0.002 PHE E 239 TYR 0.013 0.001 TYR B 289 ARG 0.008 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 395) hydrogen bonds : angle 4.89279 ( 1104) SS BOND : bond 0.00804 ( 3) SS BOND : angle 1.26476 ( 6) covalent geometry : bond 0.00340 ( 8455) covalent geometry : angle 0.57107 (11487) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.8416 (ppp) cc_final: 0.7564 (ppp) REVERT: B 72 SER cc_start: 0.8037 (t) cc_final: 0.7724 (p) REVERT: B 119 ASN cc_start: 0.8038 (m-40) cc_final: 0.7780 (m-40) REVERT: B 169 TRP cc_start: 0.8481 (OUTLIER) cc_final: 0.8113 (m-10) REVERT: B 217 MET cc_start: 0.7142 (mmt) cc_final: 0.6891 (mmt) REVERT: B 234 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6098 (t80) REVERT: B 334 SER cc_start: 0.7438 (m) cc_final: 0.6914 (t) REVERT: R 109 TYR cc_start: 0.7007 (m-80) cc_final: 0.6661 (m-80) REVERT: R 140 TYR cc_start: 0.8055 (m-80) cc_final: 0.7649 (m-80) REVERT: R 168 TRP cc_start: 0.6282 (t-100) cc_final: 0.5343 (t-100) REVERT: R 196 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7535 (mt) REVERT: E 18 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7763 (ptm160) REVERT: E 155 VAL cc_start: 0.8033 (p) cc_final: 0.7766 (t) REVERT: E 172 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7883 (p) REVERT: E 192 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7331 (mmp) REVERT: A 17 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7996 (mtpp) outliers start: 34 outliers final: 21 residues processed: 225 average time/residue: 0.9673 time to fit residues: 234.4680 Evaluate side-chains 231 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 15 optimal weight: 0.0370 chunk 2 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN E 82 GLN E 186 GLN A 221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.148436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.134307 restraints weight = 12344.281| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.06 r_work: 0.3768 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8458 Z= 0.165 Angle : 0.592 8.176 11493 Z= 0.304 Chirality : 0.044 0.223 1313 Planarity : 0.004 0.033 1444 Dihedral : 4.579 27.338 1158 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.91 % Allowed : 22.71 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1047 helix: 1.54 (0.29), residues: 326 sheet: 0.16 (0.31), residues: 260 loop : -0.39 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.006 0.001 HIS E 35 PHE 0.016 0.002 PHE E 239 TYR 0.015 0.002 TYR B 289 ARG 0.013 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 395) hydrogen bonds : angle 4.92583 ( 1104) SS BOND : bond 0.00814 ( 3) SS BOND : angle 1.31820 ( 6) covalent geometry : bond 0.00379 ( 8455) covalent geometry : angle 0.59098 (11487) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.848 Fit side-chains REVERT: B 61 MET cc_start: 0.8415 (ppp) cc_final: 0.7517 (ppp) REVERT: B 72 SER cc_start: 0.8026 (t) cc_final: 0.7711 (p) REVERT: B 111 TYR cc_start: 0.8530 (m-80) cc_final: 0.8317 (m-80) REVERT: B 119 ASN cc_start: 0.8052 (m-40) cc_final: 0.7821 (m-40) REVERT: B 169 TRP cc_start: 0.8509 (OUTLIER) cc_final: 0.8087 (m-10) REVERT: B 217 MET cc_start: 0.7102 (mmt) cc_final: 0.6849 (mmt) REVERT: B 334 SER cc_start: 0.7473 (m) cc_final: 0.6944 (t) REVERT: R 109 TYR cc_start: 0.6940 (m-80) cc_final: 0.6621 (m-80) REVERT: R 140 TYR cc_start: 0.8073 (m-80) cc_final: 0.7668 (m-80) REVERT: R 168 TRP cc_start: 0.6342 (t-100) cc_final: 0.5396 (t-100) REVERT: R 196 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7538 (mt) REVERT: E 18 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7772 (ptm160) REVERT: E 38 ARG cc_start: 0.7957 (ptt90) cc_final: 0.7736 (ptm160) REVERT: E 155 VAL cc_start: 0.8036 (p) cc_final: 0.7754 (t) REVERT: E 172 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.7892 (p) REVERT: E 192 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7317 (mmp) REVERT: A 17 LYS cc_start: 0.8187 (mtpp) cc_final: 0.7762 (mtpp) outliers start: 35 outliers final: 22 residues processed: 226 average time/residue: 0.9420 time to fit residues: 229.3178 Evaluate side-chains 233 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 58 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN E 82 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.148675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.134616 restraints weight = 12185.156| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.05 r_work: 0.3776 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8458 Z= 0.145 Angle : 0.592 11.566 11493 Z= 0.301 Chirality : 0.043 0.226 1313 Planarity : 0.004 0.049 1444 Dihedral : 4.512 27.185 1158 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.80 % Allowed : 23.04 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1047 helix: 1.59 (0.29), residues: 328 sheet: 0.13 (0.32), residues: 250 loop : -0.40 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE R 127 TYR 0.012 0.001 TYR B 59 ARG 0.007 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 395) hydrogen bonds : angle 4.88337 ( 1104) SS BOND : bond 0.00757 ( 3) SS BOND : angle 1.15803 ( 6) covalent geometry : bond 0.00332 ( 8455) covalent geometry : angle 0.59159 (11487) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.948 Fit side-chains REVERT: B 61 MET cc_start: 0.8398 (ppp) cc_final: 0.7496 (ppp) REVERT: B 72 SER cc_start: 0.8038 (t) cc_final: 0.7736 (p) REVERT: B 111 TYR cc_start: 0.8522 (m-80) cc_final: 0.8288 (m-80) REVERT: B 119 ASN cc_start: 0.8051 (m-40) cc_final: 0.7823 (m-40) REVERT: B 169 TRP cc_start: 0.8466 (OUTLIER) cc_final: 0.8099 (m-10) REVERT: B 217 MET cc_start: 0.7066 (mmt) cc_final: 0.6821 (mmt) REVERT: B 234 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.6139 (t80) REVERT: B 334 SER cc_start: 0.7446 (m) cc_final: 0.6932 (t) REVERT: R 109 TYR cc_start: 0.6928 (m-80) cc_final: 0.6607 (m-80) REVERT: R 140 TYR cc_start: 0.8063 (m-80) cc_final: 0.7699 (m-80) REVERT: R 167 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: R 168 TRP cc_start: 0.6320 (t-100) cc_final: 0.5409 (t-100) REVERT: R 196 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7507 (mt) REVERT: E 192 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7288 (mmp) REVERT: A 17 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7981 (mtpp) outliers start: 34 outliers final: 21 residues processed: 221 average time/residue: 0.9714 time to fit residues: 230.6856 Evaluate side-chains 229 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 167 ASP Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 263 LEU Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 95 optimal weight: 0.0980 chunk 69 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.150120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.135932 restraints weight = 12431.018| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.08 r_work: 0.3793 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8458 Z= 0.121 Angle : 0.571 8.226 11493 Z= 0.292 Chirality : 0.043 0.220 1313 Planarity : 0.004 0.068 1444 Dihedral : 4.411 27.073 1158 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.02 % Allowed : 23.83 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1047 helix: 1.62 (0.29), residues: 332 sheet: 0.20 (0.32), residues: 243 loop : -0.42 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.001 PHE R 326 TYR 0.012 0.001 TYR E 190 ARG 0.016 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 395) hydrogen bonds : angle 4.80766 ( 1104) SS BOND : bond 0.00642 ( 3) SS BOND : angle 0.95535 ( 6) covalent geometry : bond 0.00273 ( 8455) covalent geometry : angle 0.57062 (11487) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7334.83 seconds wall clock time: 126 minutes 44.87 seconds (7604.87 seconds total)