Starting phenix.real_space_refine on Wed Jan 15 17:49:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x16_37985/01_2025/8x16_37985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x16_37985/01_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_37985/01_2025/8x16_37985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x16_37985/01_2025/8x16_37985.map" model { file = "/net/cci-nas-00/data/ceres_data/8x16_37985/01_2025/8x16_37985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x16_37985/01_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-5571/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: 5.50, 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: 2.29 Conformation dependent library (CDL) restraints added in 1.0 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: 0.97 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: 2.57 Time building geometry restraints manager: 2.62 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: 0.930 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: 0.090 Process input model: 22.590 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- 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 : 0.974 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: 0.2455 time to fit residues: 101.1979 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 : 1.089 ------------------------------------------------------------------------------- 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 = 0.189248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.151987 restraints weight = 13511.399| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.87 r_work: 0.3813 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3982 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 7.803 12117 Z= 0.316 Chirality : 0.044 0.196 1402 Planarity : 0.004 0.063 1507 Dihedral : 4.943 86.924 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 : 15.25 % Favored : 81.66 % 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 : 1.138 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: 0.7957 (m) cc_final: 0.7420 (m) REVERT: R 173 ARG cc_start: 0.8316 (mtp-110) cc_final: 0.7934 (mtm110) REVERT: R 190 LEU cc_start: 0.8440 (tt) cc_final: 0.8054 (tt) REVERT: R 265 TYR cc_start: 0.7154 (m-80) cc_final: 0.6943 (m-80) REVERT: A 276 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 280 LYS cc_start: 0.8959 (ptmt) cc_final: 0.8631 (ptpp) REVERT: B 145 TYR cc_start: 0.8416 (p90) cc_final: 0.8214 (p90) REVERT: B 220 GLN cc_start: 0.7662 (mt0) cc_final: 0.7165 (mt0) REVERT: C 27 ARG cc_start: 0.5122 (mtt90) cc_final: 0.4656 (mmm160) REVERT: H 82 GLN cc_start: 0.7363 (pp30) cc_final: 0.6904 (mm-40) REVERT: H 230 MET cc_start: 0.6285 (ttt) cc_final: 0.6067 (ttm) outliers start: 29 outliers final: 12 residues processed: 231 average time/residue: 0.2087 time to fit residues: 66.5124 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 : 0.951 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.0000 chunk 66 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 99 optimal weight: 20.0000 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS A 322 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.188777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.146657 restraints weight = 13290.664| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.05 r_work: 0.3792 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8936 Z= 0.163 Angle : 0.544 7.696 12117 Z= 0.277 Chirality : 0.042 0.215 1402 Planarity : 0.003 0.066 1507 Dihedral : 4.669 89.230 1240 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.88 % Allowed : 16.20 % Favored : 80.92 % 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: -0.00 (0.25), residues: 1108 helix: 1.58 (0.27), residues: 391 sheet: -0.27 (0.31), residues: 260 loop : -1.23 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.017 0.001 HIS R 124 PHE 0.023 0.001 PHE A 191 TYR 0.010 0.001 TYR A 296 ARG 0.004 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 205 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.917 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: 0.8031 (m) cc_final: 0.7379 (m) REVERT: R 146 MET cc_start: 0.6316 (ttm) cc_final: 0.5916 (tmm) REVERT: R 173 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7972 (mtp85) REVERT: A 205 ARG cc_start: 0.7041 (mtm-85) cc_final: 0.6724 (mpp80) REVERT: B 105 TYR cc_start: 0.8663 (t80) cc_final: 0.8267 (t80) REVERT: B 220 GLN cc_start: 0.7626 (mt0) cc_final: 0.7260 (mt0) REVERT: B 251 ARG cc_start: 0.6890 (ttm-80) cc_final: 0.6402 (mtt-85) REVERT: H 30 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.8080 (m) REVERT: H 82 GLN cc_start: 0.7540 (pp30) cc_final: 0.6923 (mm110) REVERT: H 158 SER cc_start: 0.7283 (p) cc_final: 0.7071 (m) outliers start: 27 outliers final: 20 residues processed: 198 average time/residue: 0.2098 time to fit residues: 56.9423 Evaluate side-chains 185 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 0.0980 chunk 104 optimal weight: 0.2980 chunk 13 optimal weight: 0.1980 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.184889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.141497 restraints weight = 13121.221| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.03 r_work: 0.3733 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8936 Z= 0.179 Angle : 0.550 10.922 12117 Z= 0.280 Chirality : 0.042 0.212 1402 Planarity : 0.003 0.063 1507 Dihedral : 4.604 88.453 1240 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.94 % Allowed : 17.06 % Favored : 79.00 % 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: 0.17 (0.25), residues: 1108 helix: 1.60 (0.27), residues: 392 sheet: -0.16 (0.31), residues: 271 loop : -1.02 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 47 HIS 0.003 0.001 HIS B 54 PHE 0.031 0.001 PHE R 182 TYR 0.021 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 225 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.948 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: 0.8256 (m) cc_final: 0.7798 (m) REVERT: R 102 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8305 (tm) REVERT: R 114 LEU cc_start: 0.8602 (pp) cc_final: 0.8277 (tt) REVERT: R 146 MET cc_start: 0.6293 (ttm) cc_final: 0.5926 (tmm) REVERT: R 173 ARG cc_start: 0.8292 (mtp-110) cc_final: 0.7799 (mtm110) REVERT: R 232 LEU cc_start: 0.7307 (mp) cc_final: 0.6689 (tt) REVERT: R 277 MET cc_start: 0.6984 (ttm) cc_final: 0.6713 (ttm) REVERT: A 255 ASN cc_start: 0.7899 (m-40) cc_final: 0.7571 (m-40) REVERT: B 105 TYR cc_start: 0.8785 (t80) cc_final: 0.8582 (t80) REVERT: B 179 THR cc_start: 0.8584 (m) cc_final: 0.8355 (p) REVERT: B 220 GLN cc_start: 0.7645 (mt0) cc_final: 0.7298 (mt0) REVERT: B 292 PHE cc_start: 0.6309 (m-10) cc_final: 0.6011 (m-10) REVERT: C 27 ARG cc_start: 0.5409 (mtt90) cc_final: 0.4594 (tmt170) REVERT: H 30 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8161 (m) REVERT: H 47 TRP cc_start: 0.6995 (t60) cc_final: 0.6752 (t60) outliers start: 37 outliers final: 25 residues processed: 211 average time/residue: 0.2084 time to fit residues: 60.6492 Evaluate side-chains 193 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 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 52 GLN 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 A residue 351 CYS 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 293 ASN 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 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: 5.9990 chunk 31 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 A 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.177365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.132404 restraints weight = 12840.816| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.99 r_work: 0.3614 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8936 Z= 0.302 Angle : 0.627 10.024 12117 Z= 0.325 Chirality : 0.044 0.175 1402 Planarity : 0.004 0.059 1507 Dihedral : 4.824 80.622 1240 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.22 % Allowed : 17.06 % 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: 0.12 (0.25), residues: 1108 helix: 1.57 (0.27), residues: 394 sheet: -0.25 (0.31), residues: 275 loop : -1.02 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 185 HIS 0.013 0.002 HIS R 124 PHE 0.031 0.002 PHE R 182 TYR 0.013 0.002 TYR H 190 ARG 0.009 0.001 ARG R 126 *********************** 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 239 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8322 (m) cc_final: 0.7922 (m) REVERT: R 173 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.7812 (mtm110) REVERT: R 232 LEU cc_start: 0.7302 (mp) cc_final: 0.6692 (tt) REVERT: A 255 ASN cc_start: 0.7893 (m-40) cc_final: 0.7374 (m-40) REVERT: B 142 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.6600 (m90) REVERT: B 160 SER cc_start: 0.8331 (m) cc_final: 0.8092 (t) REVERT: B 220 GLN cc_start: 0.7698 (mt0) cc_final: 0.7376 (mt0) REVERT: B 223 THR cc_start: 0.8302 (p) cc_final: 0.8049 (p) REVERT: B 292 PHE cc_start: 0.7103 (m-10) cc_final: 0.6894 (m-10) REVERT: C 27 ARG cc_start: 0.5728 (mtt90) cc_final: 0.4685 (tmt170) REVERT: H 30 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8338 (m) REVERT: H 138 ILE cc_start: 0.6669 (mm) cc_final: 0.6384 (mm) outliers start: 49 outliers final: 32 residues processed: 217 average time/residue: 0.2043 time to fit residues: 61.0929 Evaluate side-chains 204 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 ILE 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 122 THR Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 144 THR Chi-restraints excluded: chain R residue 184 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 52 GLN 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 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 30 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 83 MET 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: 0.0970 chunk 39 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 40.0000 chunk 52 optimal weight: 0.0870 chunk 24 optimal weight: 0.0020 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.180941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.136678 restraints weight = 12779.797| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.99 r_work: 0.3669 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.6608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8936 Z= 0.152 Angle : 0.582 11.072 12117 Z= 0.288 Chirality : 0.042 0.148 1402 Planarity : 0.003 0.048 1507 Dihedral : 4.553 78.891 1240 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.41 % Allowed : 20.26 % Favored : 76.33 % 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: 0.29 (0.26), residues: 1108 helix: 1.69 (0.28), residues: 397 sheet: -0.14 (0.31), residues: 272 loop : -0.94 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP H 47 HIS 0.003 0.001 HIS R 79 PHE 0.047 0.002 PHE R 255 TYR 0.021 0.001 TYR R 15 ARG 0.003 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 203 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8358 (m) cc_final: 0.8034 (m) REVERT: R 86 MET cc_start: 0.6442 (ptt) cc_final: 0.5731 (mmt) REVERT: R 173 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7599 (mtm110) REVERT: R 232 LEU cc_start: 0.7262 (mp) cc_final: 0.6630 (tt) REVERT: A 247 MET cc_start: 0.6841 (ptt) cc_final: 0.6567 (ptm) REVERT: B 129 ARG cc_start: 0.8139 (ttt90) cc_final: 0.7744 (ttm110) REVERT: B 220 GLN cc_start: 0.7650 (mt0) cc_final: 0.7337 (mt0) REVERT: B 292 PHE cc_start: 0.6815 (m-10) cc_final: 0.6537 (m-10) REVERT: C 27 ARG cc_start: 0.5732 (mtt90) cc_final: 0.4711 (tmt170) REVERT: H 27 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6254 (p90) REVERT: H 30 SER cc_start: 0.8767 (p) cc_final: 0.8329 (m) REVERT: H 62 ASP cc_start: 0.7889 (m-30) cc_final: 0.7582 (m-30) REVERT: H 83 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6633 (ptp) REVERT: H 233 LEU cc_start: 0.8760 (tp) cc_final: 0.8480 (tp) outliers start: 32 outliers final: 22 residues processed: 185 average time/residue: 0.2089 time to fit residues: 54.4189 Evaluate side-chains 183 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 264 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 52 GLN Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 27 PHE 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 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.176775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.136649 restraints weight = 13117.436| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.92 r_work: 0.3616 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8936 Z= 0.228 Angle : 0.618 12.461 12117 Z= 0.310 Chirality : 0.044 0.164 1402 Planarity : 0.003 0.045 1507 Dihedral : 4.617 76.029 1240 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.16 % Allowed : 18.34 % Favored : 77.51 % 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: 0.36 (0.26), residues: 1108 helix: 1.74 (0.28), residues: 396 sheet: -0.06 (0.31), residues: 273 loop : -0.93 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP H 47 HIS 0.004 0.001 HIS B 54 PHE 0.030 0.002 PHE R 182 TYR 0.018 0.001 TYR R 265 ARG 0.011 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 213 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8422 (m) cc_final: 0.8153 (m) REVERT: R 86 MET cc_start: 0.6618 (ptt) cc_final: 0.5859 (mmt) REVERT: R 173 ARG cc_start: 0.8095 (mtp-110) cc_final: 0.7611 (mtm110) REVERT: R 232 LEU cc_start: 0.7447 (mp) cc_final: 0.6767 (tt) REVERT: A 247 MET cc_start: 0.7093 (ptt) cc_final: 0.6835 (ptm) REVERT: B 129 ARG cc_start: 0.8191 (ttt90) cc_final: 0.7770 (ttm110) REVERT: B 142 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7241 (m90) REVERT: B 220 GLN cc_start: 0.7631 (mt0) cc_final: 0.7314 (mt0) REVERT: C 27 ARG cc_start: 0.5920 (mtt90) cc_final: 0.4766 (tmt170) REVERT: H 27 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7029 (p90) REVERT: H 30 SER cc_start: 0.8819 (p) cc_final: 0.8397 (m) REVERT: H 62 ASP cc_start: 0.7971 (m-30) cc_final: 0.7689 (m-30) REVERT: H 233 LEU cc_start: 0.8722 (tp) cc_final: 0.8360 (tp) outliers start: 39 outliers final: 30 residues processed: 196 average time/residue: 0.1918 time to fit residues: 53.5259 Evaluate side-chains 189 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 184 THR 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 190 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 254 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 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain H residue 27 PHE 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 237 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.174328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.129082 restraints weight = 12964.025| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.96 r_work: 0.3559 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.7717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8936 Z= 0.281 Angle : 0.670 13.647 12117 Z= 0.332 Chirality : 0.045 0.204 1402 Planarity : 0.004 0.044 1507 Dihedral : 4.775 73.883 1240 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.05 % Allowed : 20.15 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1108 helix: 1.72 (0.28), residues: 393 sheet: -0.06 (0.31), residues: 278 loop : -0.97 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP H 47 HIS 0.004 0.001 HIS H 167 PHE 0.035 0.002 PHE R 182 TYR 0.025 0.002 TYR R 265 ARG 0.007 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 199 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8517 (m) cc_final: 0.8220 (m) REVERT: R 86 MET cc_start: 0.6648 (ptt) cc_final: 0.5870 (mmt) REVERT: R 173 ARG cc_start: 0.8212 (mtp-110) cc_final: 0.7802 (mtm110) REVERT: R 232 LEU cc_start: 0.7486 (mp) cc_final: 0.6814 (tt) REVERT: A 53 MET cc_start: 0.8058 (ptp) cc_final: 0.7796 (ptp) REVERT: A 247 MET cc_start: 0.7303 (ptt) cc_final: 0.7042 (ptm) REVERT: B 129 ARG cc_start: 0.8257 (ttt90) cc_final: 0.7834 (ttm110) REVERT: B 142 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7596 (m90) REVERT: B 220 GLN cc_start: 0.7769 (mt0) cc_final: 0.7459 (mt0) REVERT: B 251 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7175 (mtt-85) REVERT: C 27 ARG cc_start: 0.6049 (mtt90) cc_final: 0.4802 (tmt170) REVERT: H 27 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.7200 (p90) REVERT: H 30 SER cc_start: 0.8868 (p) cc_final: 0.8485 (m) REVERT: H 57 THR cc_start: 0.7470 (p) cc_final: 0.7147 (t) REVERT: H 62 ASP cc_start: 0.8139 (m-30) cc_final: 0.7901 (m-30) REVERT: H 233 LEU cc_start: 0.8771 (tp) cc_final: 0.8447 (tp) outliers start: 38 outliers final: 30 residues processed: 184 average time/residue: 0.1987 time to fit residues: 51.0596 Evaluate side-chains 183 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 184 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 262 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 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 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 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain H residue 27 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.176191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131111 restraints weight = 13047.621| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.01 r_work: 0.3601 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.7887 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= 0.200 Angle : 0.653 14.269 12117 Z= 0.321 Chirality : 0.043 0.161 1402 Planarity : 0.003 0.047 1507 Dihedral : 4.645 72.834 1240 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.99 % Allowed : 21.54 % Favored : 75.48 % 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: 0.41 (0.26), residues: 1108 helix: 1.80 (0.28), residues: 393 sheet: 0.03 (0.32), residues: 262 loop : -0.92 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 47 HIS 0.002 0.001 HIS H 232 PHE 0.040 0.002 PHE H 239 TYR 0.019 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 190 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8514 (m) cc_final: 0.8256 (m) REVERT: R 86 MET cc_start: 0.6651 (ptt) cc_final: 0.5720 (mmt) REVERT: R 173 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7718 (mtm110) REVERT: R 232 LEU cc_start: 0.7463 (mp) cc_final: 0.6808 (tt) REVERT: A 247 MET cc_start: 0.7356 (ptt) cc_final: 0.6870 (mtm) REVERT: B 129 ARG cc_start: 0.8272 (ttt90) cc_final: 0.7864 (ttm110) REVERT: B 220 GLN cc_start: 0.7759 (mt0) cc_final: 0.7457 (mt0) REVERT: B 251 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7164 (mtt-85) REVERT: C 27 ARG cc_start: 0.6118 (mtt90) cc_final: 0.4823 (tmt170) REVERT: H 27 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7051 (p90) REVERT: H 30 SER cc_start: 0.8811 (p) cc_final: 0.8439 (m) REVERT: H 62 ASP cc_start: 0.8097 (m-30) cc_final: 0.7852 (m-30) REVERT: H 233 LEU cc_start: 0.8707 (tp) cc_final: 0.8315 (tp) outliers start: 28 outliers final: 24 residues processed: 177 average time/residue: 0.2112 time to fit residues: 51.5738 Evaluate side-chains 178 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 A residue 34 VAL Chi-restraints excluded: chain A residue 190 THR 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 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 38 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** H 39 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 = 0.4266 r_free = 0.4266 target = 0.177378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132549 restraints weight = 12882.292| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.01 r_work: 0.3622 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.7973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8936 Z= 0.183 Angle : 0.643 13.821 12117 Z= 0.317 Chirality : 0.043 0.162 1402 Planarity : 0.003 0.047 1507 Dihedral : 4.550 71.170 1240 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.77 % Allowed : 22.49 % Favored : 74.73 % 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: 0.47 (0.26), residues: 1108 helix: 1.85 (0.28), residues: 393 sheet: 0.05 (0.32), residues: 263 loop : -0.89 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP H 47 HIS 0.002 0.001 HIS R 95 PHE 0.033 0.002 PHE H 239 TYR 0.026 0.001 TYR A 296 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: 26 poor density : 157 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8509 (m) cc_final: 0.8253 (m) REVERT: R 86 MET cc_start: 0.6616 (ptt) cc_final: 0.5995 (mmt) REVERT: R 173 ARG cc_start: 0.8172 (mtp-110) cc_final: 0.7907 (mtp-110) REVERT: R 188 ILE cc_start: 0.9000 (mm) cc_final: 0.8755 (mt) REVERT: R 232 LEU cc_start: 0.7404 (mp) cc_final: 0.6737 (tt) REVERT: R 258 GLU cc_start: 0.6355 (pp20) cc_final: 0.5906 (pm20) REVERT: A 247 MET cc_start: 0.7357 (ptt) cc_final: 0.6986 (mtp) REVERT: B 129 ARG cc_start: 0.8292 (ttt90) cc_final: 0.7868 (ttm110) REVERT: B 251 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7092 (mtt-85) REVERT: C 27 ARG cc_start: 0.6112 (mtt90) cc_final: 0.4805 (tmt170) REVERT: H 27 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.7065 (p90) REVERT: H 30 SER cc_start: 0.8803 (p) cc_final: 0.8474 (m) REVERT: H 62 ASP cc_start: 0.8103 (m-30) cc_final: 0.7797 (m-30) REVERT: H 233 LEU cc_start: 0.8676 (tp) cc_final: 0.8274 (tp) outliers start: 26 outliers final: 22 residues processed: 171 average time/residue: 0.2070 time to fit residues: 48.9636 Evaluate side-chains 175 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 321 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 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 27 PHE 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: 9.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.0050 chunk 93 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 75 optimal weight: 0.0170 chunk 99 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.6834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** H 39 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 = 0.4264 r_free = 0.4264 target = 0.176678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132224 restraints weight = 13248.157| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.01 r_work: 0.3625 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.8108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8936 Z= 0.180 Angle : 0.630 13.710 12117 Z= 0.311 Chirality : 0.043 0.167 1402 Planarity : 0.003 0.042 1507 Dihedral : 4.463 69.325 1240 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.88 % Allowed : 22.71 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1108 helix: 1.94 (0.28), residues: 393 sheet: 0.14 (0.32), residues: 263 loop : -0.86 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP H 47 HIS 0.003 0.001 HIS H 232 PHE 0.030 0.002 PHE R 182 TYR 0.025 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: 4933.64 seconds wall clock time: 88 minutes 19.43 seconds (5299.43 seconds total)