Starting phenix.real_space_refine on Thu Mar 13 05:12:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x16_37985/03_2025/8x16_37985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x16_37985/03_2025/8x16_37985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x16_37985/03_2025/8x16_37985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x16_37985/03_2025/8x16_37985.map" model { file = "/net/cci-nas-00/data/ceres_data/8x16_37985/03_2025/8x16_37985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x16_37985/03_2025/8x16_37985.cif" } resolution = 3.29 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= 0.006 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians I 1 10.91 5 S 68 5.16 5 C 5615 2.51 5 N 1468 2.21 5 O 1599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8751 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2268 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'Q8L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.47, per 1000 atoms: 0.63 Number of scatterers: 8751 At special positions: 0 Unit cell: (118.656, 92.288, 134.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) I 1 52.95 S 68 16.00 O 1599 8.00 N 1468 7.00 C 5615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 166 " distance=2.06 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.7% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'R' and resid 9 through 40 Processing helix chain 'R' and resid 41 through 44 Processing helix chain 'R' and resid 47 through 64 removed outlier: 4.058A pdb=" N ILE R 51 " --> pdb=" O THR R 47 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 75 Processing helix chain 'R' and resid 79 through 114 removed outlier: 4.947A pdb=" N PHE R 85 " --> pdb=" O TYR R 81 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 123 through 143 Processing helix chain 'R' and resid 144 through 148 Processing helix chain 'R' and resid 181 through 186 Processing helix chain 'R' and resid 186 through 209 Processing helix chain 'R' and resid 223 through 255 Proline residue: R 245 - end of helix Processing helix chain 'R' and resid 260 through 282 removed outlier: 3.840A pdb=" N ASN R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER R 275 " --> pdb=" O SER R 271 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET R 276 " --> pdb=" O HIS R 272 " (cutoff:3.500A) Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 283 through 287 removed outlier: 3.745A pdb=" N ILE R 286 " --> pdb=" O ALA R 283 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS R 287 " --> pdb=" O TYR R 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 283 through 287' Processing helix chain 'R' and resid 288 through 299 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.538A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.751A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.007A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.746A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.662A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.651A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.889A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.747A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.954A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.599A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 77 through 78 removed outlier: 3.588A pdb=" N LEU R 164 " --> pdb=" O ILE R 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 191 removed outlier: 7.773A pdb=" N GLY A 183 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY A 202 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.611A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.129A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.058A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.674A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.613A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.068A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.648A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.781A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.909A pdb=" N CYS H 159 " --> pdb=" O PHE H 212 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.770A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1194 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: 2.49 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 2836 1.37 - 1.55: 5994 1.55 - 1.74: 4 1.74 - 1.92: 101 1.92 - 2.11: 1 Bond restraints: 8936 Sorted by residual: bond pdb=" C5 Q8L R 401 " pdb=" O3 Q8L R 401 " ideal model delta sigma weight residual 1.419 1.667 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C1 Q8L R 401 " pdb=" C5 Q8L R 401 " ideal model delta sigma weight residual 1.530 1.286 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C2 Q8L R 401 " pdb=" O3 Q8L R 401 " ideal model delta sigma weight residual 1.432 1.299 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" N Q8L R 401 " pdb=" C3 Q8L R 401 " ideal model delta sigma weight residual 1.338 1.452 -0.114 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C10 Q8L R 401 " pdb=" N5 Q8L R 401 " ideal model delta sigma weight residual 1.347 1.454 -0.107 2.00e-02 2.50e+03 2.88e+01 ... (remaining 8931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 12064 2.94 - 5.89: 40 5.89 - 8.83: 9 8.83 - 11.78: 3 11.78 - 14.72: 1 Bond angle restraints: 12117 Sorted by residual: angle pdb=" C GLN R 167 " pdb=" N PHE R 168 " pdb=" CA PHE R 168 " ideal model delta sigma weight residual 121.54 136.26 -14.72 1.91e+00 2.74e-01 5.94e+01 angle pdb=" CA GLN R 167 " pdb=" C GLN R 167 " pdb=" O GLN R 167 " ideal model delta sigma weight residual 120.52 111.74 8.78 1.39e+00 5.18e-01 3.99e+01 angle pdb=" N SER R 82 " pdb=" CA SER R 82 " pdb=" C SER R 82 " ideal model delta sigma weight residual 111.02 101.47 9.55 1.52e+00 4.33e-01 3.95e+01 angle pdb=" N TYR R 81 " pdb=" CA TYR R 81 " pdb=" C TYR R 81 " ideal model delta sigma weight residual 112.97 106.71 6.26 1.06e+00 8.90e-01 3.49e+01 angle pdb=" N CYS R 166 " pdb=" CA CYS R 166 " pdb=" C CYS R 166 " ideal model delta sigma weight residual 108.73 116.17 -7.44 1.63e+00 3.76e-01 2.08e+01 ... (remaining 12112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5113 17.60 - 35.21: 140 35.21 - 52.81: 27 52.81 - 70.42: 2 70.42 - 88.02: 1 Dihedral angle restraints: 5283 sinusoidal: 2009 harmonic: 3274 Sorted by residual: dihedral pdb=" C SER R 82 " pdb=" N SER R 82 " pdb=" CA SER R 82 " pdb=" CB SER R 82 " ideal model delta harmonic sigma weight residual -122.60 -115.20 -7.40 0 2.50e+00 1.60e-01 8.76e+00 dihedral pdb=" CA SER R 242 " pdb=" C SER R 242 " pdb=" N TRP R 243 " pdb=" CA TRP R 243 " ideal model delta harmonic sigma weight residual -180.00 -166.08 -13.92 0 5.00e+00 4.00e-02 7.75e+00 dihedral pdb=" N GLN R 167 " pdb=" CA GLN R 167 " pdb=" CB GLN R 167 " pdb=" CG GLN R 167 " ideal model delta sinusoidal sigma weight residual -180.00 -136.96 -43.04 3 1.50e+01 4.44e-03 7.73e+00 ... (remaining 5280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1268 0.062 - 0.124: 125 0.124 - 0.186: 5 0.186 - 0.248: 1 0.248 - 0.310: 3 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CG LEU R 164 " pdb=" CB LEU R 164 " pdb=" CD1 LEU R 164 " pdb=" CD2 LEU R 164 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA LEU R 164 " pdb=" N LEU R 164 " pdb=" C LEU R 164 " pdb=" CB LEU R 164 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA CYS R 166 " pdb=" N CYS R 166 " pdb=" C CYS R 166 " pdb=" CB CYS R 166 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1399 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 80 " -0.013 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C PHE R 80 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE R 80 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR R 81 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 235 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO H 236 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO H 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 164 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C LEU R 164 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU R 164 " 0.009 2.00e-02 2.50e+03 pdb=" N SER R 165 " 0.008 2.00e-02 2.50e+03 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.75: 966 2.75 - 3.31: 8970 3.31 - 3.86: 15001 3.86 - 4.41: 17966 4.41 - 4.96: 30929 Nonbonded interactions: 73832 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.203 3.040 nonbonded pdb=" CD1 PHE R 182 " pdb=" OG SER R 247 " model vdw 2.260 3.340 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.287 3.040 nonbonded pdb=" O VAL R 141 " pdb=" OH TYR R 176 " model vdw 2.292 3.040 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.313 3.120 ... (remaining 73827 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.190 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.248 8936 Z= 0.308 Angle : 0.531 14.721 12117 Z= 0.302 Chirality : 0.041 0.310 1402 Planarity : 0.003 0.037 1507 Dihedral : 8.098 88.024 3168 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.99 % Favored : 97.92 % Rotamer: Outliers : 0.32 % Allowed : 4.80 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1108 helix: 0.28 (0.25), residues: 396 sheet: -0.61 (0.30), residues: 263 loop : -1.82 (0.25), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.002 0.000 HIS H 35 PHE 0.009 0.001 PHE A 189 TYR 0.006 0.001 TYR H 102 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 311 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.6825 (m) cc_final: 0.6518 (m) REVERT: R 175 ASP cc_start: 0.7181 (p0) cc_final: 0.6514 (p0) REVERT: A 302 TYR cc_start: 0.7277 (t80) cc_final: 0.6885 (t80) outliers start: 3 outliers final: 1 residues processed: 314 average time/residue: 0.2511 time to fit residues: 103.7427 Evaluate side-chains 188 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 124 HIS B 16 ASN B 293 ASN C 24 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.189244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.147254 restraints weight = 13480.019| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.08 r_work: 0.3798 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8936 Z= 0.256 Angle : 0.613 7.801 12117 Z= 0.316 Chirality : 0.044 0.196 1402 Planarity : 0.004 0.063 1507 Dihedral : 4.943 86.922 1242 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.09 % Allowed : 15.14 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1108 helix: 1.20 (0.27), residues: 395 sheet: -0.38 (0.30), residues: 266 loop : -1.54 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 243 HIS 0.004 0.001 HIS B 54 PHE 0.024 0.002 PHE H 68 TYR 0.017 0.002 TYR R 265 ARG 0.006 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.7967 (m) cc_final: 0.7433 (m) REVERT: R 173 ARG cc_start: 0.8318 (mtp-110) cc_final: 0.7937 (mtm110) REVERT: R 190 LEU cc_start: 0.8447 (tt) cc_final: 0.8073 (tt) REVERT: R 265 TYR cc_start: 0.7157 (m-80) cc_final: 0.6949 (m-80) REVERT: A 276 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7642 (tm-30) REVERT: A 280 LYS cc_start: 0.8974 (ptmt) cc_final: 0.8637 (ptpp) REVERT: B 145 TYR cc_start: 0.8423 (p90) cc_final: 0.8217 (p90) REVERT: B 220 GLN cc_start: 0.7681 (mt0) cc_final: 0.7176 (mt0) REVERT: C 27 ARG cc_start: 0.5115 (mtt90) cc_final: 0.4637 (mmm160) REVERT: H 82 GLN cc_start: 0.7365 (pp30) cc_final: 0.6908 (mm-40) REVERT: H 230 MET cc_start: 0.6279 (ttt) cc_final: 0.6064 (ttm) outliers start: 29 outliers final: 12 residues processed: 231 average time/residue: 0.2004 time to fit residues: 63.6925 Evaluate side-chains 188 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.0270 chunk 66 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.186899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.144247 restraints weight = 13100.955| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.04 r_work: 0.3765 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8936 Z= 0.183 Angle : 0.549 7.637 12117 Z= 0.281 Chirality : 0.042 0.244 1402 Planarity : 0.004 0.066 1507 Dihedral : 4.718 89.820 1240 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.77 % Allowed : 16.20 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1108 helix: 1.61 (0.27), residues: 390 sheet: -0.24 (0.31), residues: 266 loop : -1.20 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.026 0.001 HIS R 124 PHE 0.024 0.002 PHE A 191 TYR 0.011 0.001 TYR A 296 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8047 (m) cc_final: 0.7413 (m) REVERT: R 102 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8176 (tm) REVERT: R 113 LYS cc_start: 0.8394 (mmmt) cc_final: 0.8192 (mtpt) REVERT: R 146 MET cc_start: 0.6248 (ttm) cc_final: 0.6020 (tmm) REVERT: R 173 ARG cc_start: 0.8317 (mtp-110) cc_final: 0.7971 (mtp85) REVERT: A 205 ARG cc_start: 0.7086 (mtm-85) cc_final: 0.6763 (mpp80) REVERT: A 315 ASP cc_start: 0.8079 (p0) cc_final: 0.7864 (p0) REVERT: B 105 TYR cc_start: 0.8713 (t80) cc_final: 0.8288 (t80) REVERT: B 220 GLN cc_start: 0.7648 (mt0) cc_final: 0.7299 (mt0) REVERT: B 251 ARG cc_start: 0.6996 (ttm-80) cc_final: 0.6446 (mtt-85) REVERT: C 27 ARG cc_start: 0.5358 (mtt90) cc_final: 0.4521 (tmt170) REVERT: H 30 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8068 (m) REVERT: H 82 GLN cc_start: 0.7606 (pp30) cc_final: 0.6947 (mm110) REVERT: H 158 SER cc_start: 0.7353 (p) cc_final: 0.7144 (m) outliers start: 26 outliers final: 17 residues processed: 204 average time/residue: 0.2120 time to fit residues: 58.8353 Evaluate side-chains 187 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 107 ASP Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 86 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 124 HIS ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.185879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.146558 restraints weight = 13216.717| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.97 r_work: 0.3752 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8936 Z= 0.161 Angle : 0.538 9.279 12117 Z= 0.275 Chirality : 0.042 0.216 1402 Planarity : 0.003 0.061 1507 Dihedral : 4.556 88.583 1240 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.52 % Allowed : 18.02 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1108 helix: 1.61 (0.27), residues: 392 sheet: -0.15 (0.31), residues: 270 loop : -1.06 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 47 HIS 0.002 0.001 HIS B 54 PHE 0.030 0.001 PHE R 182 TYR 0.019 0.001 TYR A 230 ARG 0.004 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8263 (m) cc_final: 0.7771 (m) REVERT: R 102 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8200 (tm) REVERT: R 146 MET cc_start: 0.6298 (ttm) cc_final: 0.5794 (tmm) REVERT: R 173 ARG cc_start: 0.8330 (mtp-110) cc_final: 0.7907 (mtm110) REVERT: R 232 LEU cc_start: 0.7288 (mp) cc_final: 0.6676 (tt) REVERT: R 277 MET cc_start: 0.6940 (ttm) cc_final: 0.6654 (ttm) REVERT: A 255 ASN cc_start: 0.7779 (m-40) cc_final: 0.7467 (m-40) REVERT: A 315 ASP cc_start: 0.8173 (p0) cc_final: 0.7894 (p0) REVERT: B 179 THR cc_start: 0.8613 (m) cc_final: 0.8381 (p) REVERT: B 220 GLN cc_start: 0.7607 (mt0) cc_final: 0.7257 (mt0) REVERT: B 292 PHE cc_start: 0.6300 (m-10) cc_final: 0.6027 (m-10) REVERT: C 27 ARG cc_start: 0.5308 (mtt90) cc_final: 0.4564 (tmt170) REVERT: H 47 TRP cc_start: 0.6930 (t60) cc_final: 0.6668 (t60) REVERT: H 82 GLN cc_start: 0.7558 (pp30) cc_final: 0.6984 (mm-40) outliers start: 33 outliers final: 21 residues processed: 200 average time/residue: 0.2157 time to fit residues: 59.6007 Evaluate side-chains 182 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 242 SER Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 13 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 124 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.178804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134230 restraints weight = 12857.223| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.97 r_work: 0.3637 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8936 Z= 0.267 Angle : 0.630 12.589 12117 Z= 0.319 Chirality : 0.044 0.276 1402 Planarity : 0.004 0.054 1507 Dihedral : 4.806 83.809 1240 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.69 % Allowed : 17.59 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.14 (0.25), residues: 1108 helix: 1.56 (0.27), residues: 393 sheet: -0.19 (0.31), residues: 273 loop : -1.04 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 185 HIS 0.020 0.002 HIS R 124 PHE 0.030 0.002 PHE R 182 TYR 0.014 0.002 TYR A 230 ARG 0.009 0.001 ARG R 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 16 ILE cc_start: 0.8800 (mm) cc_final: 0.8333 (mm) REVERT: R 25 CYS cc_start: 0.8341 (m) cc_final: 0.7923 (m) REVERT: R 173 ARG cc_start: 0.8160 (mtp-110) cc_final: 0.7706 (mtm110) REVERT: R 232 LEU cc_start: 0.7275 (mp) cc_final: 0.6668 (tt) REVERT: A 255 ASN cc_start: 0.7869 (m-40) cc_final: 0.7360 (m-40) REVERT: A 315 ASP cc_start: 0.8315 (p0) cc_final: 0.8055 (p0) REVERT: B 220 GLN cc_start: 0.7693 (mt0) cc_final: 0.7373 (mt0) REVERT: B 223 THR cc_start: 0.8351 (p) cc_final: 0.8101 (p) REVERT: B 292 PHE cc_start: 0.6943 (m-10) cc_final: 0.6700 (m-10) REVERT: C 27 ARG cc_start: 0.5651 (mtt90) cc_final: 0.4678 (tmt170) REVERT: H 30 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8326 (m) outliers start: 44 outliers final: 30 residues processed: 210 average time/residue: 0.1926 time to fit residues: 56.5634 Evaluate side-chains 191 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 280 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 0.0670 chunk 52 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.176487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.131350 restraints weight = 12740.651| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.96 r_work: 0.3600 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.6939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8936 Z= 0.241 Angle : 0.629 10.473 12117 Z= 0.313 Chirality : 0.043 0.149 1402 Planarity : 0.004 0.048 1507 Dihedral : 4.774 78.946 1240 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.69 % Allowed : 18.44 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1108 helix: 1.59 (0.27), residues: 397 sheet: -0.17 (0.31), residues: 273 loop : -1.02 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 47 HIS 0.006 0.001 HIS B 54 PHE 0.048 0.002 PHE R 255 TYR 0.025 0.002 TYR R 15 ARG 0.010 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8350 (m) cc_final: 0.8041 (m) REVERT: R 86 MET cc_start: 0.6465 (ptt) cc_final: 0.5813 (mmt) REVERT: R 173 ARG cc_start: 0.8029 (mtp-110) cc_final: 0.7723 (mtm110) REVERT: R 232 LEU cc_start: 0.7303 (mp) cc_final: 0.6711 (tt) REVERT: A 247 MET cc_start: 0.6991 (ptt) cc_final: 0.6718 (ptm) REVERT: A 255 ASN cc_start: 0.7943 (m-40) cc_final: 0.7481 (m-40) REVERT: A 315 ASP cc_start: 0.8447 (p0) cc_final: 0.8185 (p0) REVERT: B 129 ARG cc_start: 0.8217 (ttt90) cc_final: 0.7783 (ttm110) REVERT: B 142 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.6972 (m90) REVERT: B 220 GLN cc_start: 0.7627 (mt0) cc_final: 0.7314 (mt0) REVERT: C 27 ARG cc_start: 0.5829 (mtt90) cc_final: 0.4718 (tmt170) REVERT: H 30 SER cc_start: 0.8821 (p) cc_final: 0.8399 (m) REVERT: H 62 ASP cc_start: 0.7975 (m-30) cc_final: 0.7692 (m-30) REVERT: H 87 ARG cc_start: 0.7432 (mtt90) cc_final: 0.7176 (mtt90) REVERT: H 233 LEU cc_start: 0.8745 (tp) cc_final: 0.8525 (tp) outliers start: 44 outliers final: 32 residues processed: 200 average time/residue: 0.2109 time to fit residues: 58.6233 Evaluate side-chains 194 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 89 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 93 optimal weight: 0.0010 chunk 102 optimal weight: 0.2980 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 239 ASN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.179396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.135284 restraints weight = 13146.305| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.01 r_work: 0.3660 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.7097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8936 Z= 0.164 Angle : 0.596 12.332 12117 Z= 0.294 Chirality : 0.042 0.156 1402 Planarity : 0.003 0.048 1507 Dihedral : 4.537 77.010 1240 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.20 % Allowed : 20.15 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1108 helix: 1.67 (0.27), residues: 397 sheet: -0.11 (0.31), residues: 271 loop : -0.87 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP H 47 HIS 0.002 0.000 HIS H 35 PHE 0.031 0.002 PHE R 182 TYR 0.021 0.001 TYR R 265 ARG 0.008 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8408 (m) cc_final: 0.8159 (m) REVERT: R 86 MET cc_start: 0.6431 (ptt) cc_final: 0.5644 (mmt) REVERT: R 173 ARG cc_start: 0.8055 (mtp-110) cc_final: 0.7785 (mtm110) REVERT: R 232 LEU cc_start: 0.7363 (mp) cc_final: 0.6706 (tt) REVERT: R 256 ASN cc_start: 0.8857 (m-40) cc_final: 0.8649 (m-40) REVERT: A 247 MET cc_start: 0.6917 (ptt) cc_final: 0.6672 (ptm) REVERT: A 315 ASP cc_start: 0.8426 (p0) cc_final: 0.8157 (p0) REVERT: B 129 ARG cc_start: 0.8182 (ttt90) cc_final: 0.7844 (ttm110) REVERT: B 220 GLN cc_start: 0.7614 (mt0) cc_final: 0.7297 (mt0) REVERT: C 27 ARG cc_start: 0.5839 (mtt90) cc_final: 0.4745 (tmt170) REVERT: H 30 SER cc_start: 0.8793 (p) cc_final: 0.8382 (m) REVERT: H 62 ASP cc_start: 0.7930 (m-30) cc_final: 0.7625 (m-30) REVERT: H 87 ARG cc_start: 0.7445 (mtt90) cc_final: 0.7214 (mtt90) REVERT: H 233 LEU cc_start: 0.8747 (tp) cc_final: 0.8404 (tp) outliers start: 30 outliers final: 22 residues processed: 184 average time/residue: 0.2009 time to fit residues: 51.5967 Evaluate side-chains 182 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 147 PHE Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 237 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 69 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.178737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134210 restraints weight = 13099.625| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.03 r_work: 0.3644 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.7286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8936 Z= 0.175 Angle : 0.608 13.927 12117 Z= 0.298 Chirality : 0.042 0.162 1402 Planarity : 0.003 0.045 1507 Dihedral : 4.533 76.236 1240 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.41 % Allowed : 20.04 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1108 helix: 1.76 (0.27), residues: 397 sheet: 0.08 (0.32), residues: 269 loop : -0.88 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.050 0.002 PHE R 255 TYR 0.021 0.001 TYR R 265 ARG 0.008 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8402 (m) cc_final: 0.8146 (m) REVERT: R 172 MET cc_start: 0.8619 (mtm) cc_final: 0.8176 (mpp) REVERT: R 173 ARG cc_start: 0.8089 (mtp-110) cc_final: 0.7805 (mtm110) REVERT: R 232 LEU cc_start: 0.7391 (mp) cc_final: 0.6724 (tt) REVERT: A 247 MET cc_start: 0.6990 (ptt) cc_final: 0.6762 (ptm) REVERT: A 315 ASP cc_start: 0.8549 (p0) cc_final: 0.8246 (p0) REVERT: B 129 ARG cc_start: 0.8216 (ttt90) cc_final: 0.7867 (ttm110) REVERT: B 220 GLN cc_start: 0.7758 (mt0) cc_final: 0.7447 (mt0) REVERT: C 27 ARG cc_start: 0.5898 (mtt90) cc_final: 0.4797 (tmt170) REVERT: H 30 SER cc_start: 0.8795 (p) cc_final: 0.8373 (m) REVERT: H 62 ASP cc_start: 0.8048 (m-30) cc_final: 0.7761 (m-30) REVERT: H 87 ARG cc_start: 0.7450 (mtt90) cc_final: 0.7230 (mtt90) REVERT: H 233 LEU cc_start: 0.8770 (tp) cc_final: 0.8447 (tp) outliers start: 32 outliers final: 28 residues processed: 179 average time/residue: 0.1930 time to fit residues: 48.7573 Evaluate side-chains 185 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 147 PHE Chi-restraints excluded: chain R residue 151 MET Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 265 TYR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 280 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 0.0030 chunk 71 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.179003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137488 restraints weight = 13174.346| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.11 r_work: 0.3650 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.7454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8936 Z= 0.169 Angle : 0.609 14.990 12117 Z= 0.298 Chirality : 0.042 0.152 1402 Planarity : 0.003 0.042 1507 Dihedral : 4.488 74.711 1240 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.77 % Allowed : 21.00 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1108 helix: 1.83 (0.27), residues: 398 sheet: 0.18 (0.32), residues: 264 loop : -0.89 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.048 0.002 PHE R 255 TYR 0.020 0.001 TYR R 265 ARG 0.008 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8477 (m) cc_final: 0.8197 (m) REVERT: R 173 ARG cc_start: 0.8198 (mtp-110) cc_final: 0.7887 (mtm110) REVERT: R 232 LEU cc_start: 0.7388 (mp) cc_final: 0.6713 (tt) REVERT: A 247 MET cc_start: 0.7058 (ptt) cc_final: 0.6836 (ptm) REVERT: A 315 ASP cc_start: 0.8556 (p0) cc_final: 0.8248 (p0) REVERT: B 129 ARG cc_start: 0.8216 (ttt90) cc_final: 0.7864 (ttm110) REVERT: C 27 ARG cc_start: 0.5943 (mtt90) cc_final: 0.4810 (tmt170) REVERT: H 30 SER cc_start: 0.8814 (p) cc_final: 0.8385 (m) REVERT: H 62 ASP cc_start: 0.8076 (m-30) cc_final: 0.7796 (m-30) REVERT: H 87 ARG cc_start: 0.7463 (mtt90) cc_final: 0.7263 (mtt90) REVERT: H 233 LEU cc_start: 0.8722 (tp) cc_final: 0.8327 (tp) outliers start: 26 outliers final: 24 residues processed: 175 average time/residue: 0.1944 time to fit residues: 47.5575 Evaluate side-chains 179 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 147 PHE Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 151 MET Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 265 TYR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 83 optimal weight: 0.1980 chunk 103 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 105 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.179364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135169 restraints weight = 13057.476| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.02 r_work: 0.3644 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.7581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8936 Z= 0.168 Angle : 0.617 15.426 12117 Z= 0.299 Chirality : 0.042 0.164 1402 Planarity : 0.003 0.043 1507 Dihedral : 4.419 73.444 1240 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.88 % Allowed : 20.58 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.26), residues: 1108 helix: 1.83 (0.27), residues: 399 sheet: 0.29 (0.32), residues: 262 loop : -0.87 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP H 47 HIS 0.002 0.000 HIS H 35 PHE 0.050 0.002 PHE R 255 TYR 0.018 0.001 TYR R 265 ARG 0.007 0.000 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8506 (m) cc_final: 0.8226 (m) REVERT: R 173 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7864 (mtm110) REVERT: R 232 LEU cc_start: 0.7343 (mp) cc_final: 0.6670 (tt) REVERT: A 247 MET cc_start: 0.7208 (ptt) cc_final: 0.6983 (ptm) REVERT: A 315 ASP cc_start: 0.8577 (p0) cc_final: 0.8262 (p0) REVERT: B 129 ARG cc_start: 0.8231 (ttt90) cc_final: 0.7847 (ttm110) REVERT: H 30 SER cc_start: 0.8826 (p) cc_final: 0.8424 (m) REVERT: H 62 ASP cc_start: 0.8074 (m-30) cc_final: 0.7783 (m-30) REVERT: H 87 ARG cc_start: 0.7520 (mtt90) cc_final: 0.7315 (mtt90) REVERT: H 233 LEU cc_start: 0.8662 (tp) cc_final: 0.8240 (tp) outliers start: 27 outliers final: 24 residues processed: 171 average time/residue: 0.2008 time to fit residues: 47.9200 Evaluate side-chains 175 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 PHE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 147 PHE Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 151 MET Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 265 TYR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 0.0270 chunk 93 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.178262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.133943 restraints weight = 13089.543| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 3.00 r_work: 0.3633 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.7780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8936 Z= 0.177 Angle : 0.625 15.492 12117 Z= 0.305 Chirality : 0.043 0.182 1402 Planarity : 0.003 0.042 1507 Dihedral : 4.437 72.399 1240 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.99 % Allowed : 21.11 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 1108 helix: 1.84 (0.27), residues: 398 sheet: 0.34 (0.32), residues: 262 loop : -0.89 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.048 0.002 PHE R 255 TYR 0.016 0.001 TYR A 296 ARG 0.007 0.000 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4965.28 seconds wall clock time: 87 minutes 12.48 seconds (5232.48 seconds total)