Starting phenix.real_space_refine on Fri Oct 10 19:15:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x16_37985/10_2025/8x16_37985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x16_37985/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8x16_37985/10_2025/8x16_37985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x16_37985/10_2025/8x16_37985.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x16_37985/10_2025/8x16_37985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x16_37985/10_2025/8x16_37985.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, '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, 'ASP:plan': 1, 'ARG: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, 'ASP:plan': 2, 'ARG: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: 2.22, per 1000 atoms: 0.25 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: 0.66 Conformation dependent library (CDL) restraints added in 294.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.22 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: 1.22 Time building geometry restraints manager: 0.85 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: 1.600 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.720 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.840 ------------------------------------------------------------------------------- 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 8937 Z= 0.271 Angle : 0.535 14.721 12119 Z= 0.304 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 : 8.39 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 22 TYR 0.006 0.001 TYR H 102 PHE 0.009 0.001 PHE A 189 TRP 0.007 0.001 TRP B 297 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 8936) covalent geometry : angle 0.53132 (12117) SS BOND : bond 0.02562 ( 1) SS BOND : angle 4.76802 ( 2) hydrogen bonds : bond 0.14681 ( 425) hydrogen bonds : angle 4.59783 ( 1194) *********************** 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 : 0.323 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: 0.1002 time to fit residues: 41.8456 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 : 0.239 ------------------------------------------------------------------------------- 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 108 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 311 ASN B 16 ASN B 293 ASN C 24 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.190656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.148956 restraints weight = 13460.561| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 3.09 r_work: 0.3818 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8937 Z= 0.163 Angle : 0.630 8.612 12119 Z= 0.323 Chirality : 0.044 0.207 1402 Planarity : 0.005 0.068 1507 Dihedral : 4.926 86.711 1242 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.30 % Allowed : 14.61 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.24), residues: 1108 helix: 1.19 (0.27), residues: 395 sheet: -0.41 (0.30), residues: 260 loop : -1.51 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.020 0.002 TYR H 60 PHE 0.021 0.002 PHE A 191 TRP 0.015 0.002 TRP R 243 HIS 0.004 0.001 HIS R 158 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8936) covalent geometry : angle 0.62944 (12117) SS BOND : bond 0.00219 ( 1) SS BOND : angle 1.50166 ( 2) hydrogen bonds : bond 0.03459 ( 425) hydrogen bonds : angle 4.13008 ( 1194) *********************** 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 243 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.311 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: 0.8008 (m) cc_final: 0.7462 (m) REVERT: R 146 MET cc_start: 0.7148 (mtp) cc_final: 0.5970 (tmm) REVERT: R 168 PHE cc_start: 0.8031 (t80) cc_final: 0.7802 (t80) REVERT: R 173 ARG cc_start: 0.8312 (mtp-110) cc_final: 0.7680 (mtm110) REVERT: R 197 TYR cc_start: 0.7187 (m-80) cc_final: 0.6271 (m-80) REVERT: A 276 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 280 LYS cc_start: 0.8991 (ptmt) cc_final: 0.8717 (ptpp) REVERT: B 145 TYR cc_start: 0.8384 (p90) cc_final: 0.8072 (p90) REVERT: B 220 GLN cc_start: 0.7688 (mt0) cc_final: 0.7225 (mt0) REVERT: B 251 ARG cc_start: 0.7020 (mtm-85) cc_final: 0.6613 (mtm-85) REVERT: C 27 ARG cc_start: 0.5207 (mtt90) cc_final: 0.4675 (mmm160) REVERT: H 30 SER cc_start: 0.8256 (p) cc_final: 0.7981 (m) REVERT: H 82 GLN cc_start: 0.7330 (pp30) cc_final: 0.6830 (mm110) REVERT: H 83 MET cc_start: 0.6968 (ppp) cc_final: 0.6768 (ptp) outliers start: 31 outliers final: 12 residues processed: 232 average time/residue: 0.0850 time to fit residues: 27.5011 Evaluate side-chains 183 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 78 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 0.0870 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS R 167 GLN A 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.187052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.144742 restraints weight = 12836.818| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 3.02 r_work: 0.3773 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8937 Z= 0.126 Angle : 0.571 14.245 12119 Z= 0.288 Chirality : 0.042 0.237 1402 Planarity : 0.004 0.067 1507 Dihedral : 4.724 89.101 1240 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.30 % Allowed : 17.27 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.25), residues: 1108 helix: 1.56 (0.27), residues: 391 sheet: -0.14 (0.31), residues: 264 loop : -1.24 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.011 0.001 TYR H 190 PHE 0.023 0.002 PHE A 191 TRP 0.014 0.001 TRP B 169 HIS 0.016 0.001 HIS R 124 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8936) covalent geometry : angle 0.57045 (12117) SS BOND : bond 0.00977 ( 1) SS BOND : angle 2.57798 ( 2) hydrogen bonds : bond 0.03156 ( 425) hydrogen bonds : angle 3.92538 ( 1194) *********************** 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 208 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8068 (m) cc_final: 0.7446 (m) REVERT: R 146 MET cc_start: 0.6693 (mtp) cc_final: 0.6344 (tmm) REVERT: R 173 ARG cc_start: 0.8337 (mtp-110) cc_final: 0.7971 (mtp85) REVERT: R 197 TYR cc_start: 0.7207 (m-80) cc_final: 0.6467 (m-80) REVERT: A 276 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 280 LYS cc_start: 0.8999 (ptmt) cc_final: 0.8719 (ptpp) REVERT: A 315 ASP cc_start: 0.8091 (p0) cc_final: 0.7878 (p0) REVERT: B 105 TYR cc_start: 0.8695 (t80) cc_final: 0.8246 (t80) REVERT: B 220 GLN cc_start: 0.7705 (mt0) cc_final: 0.7362 (mt0) REVERT: B 251 ARG cc_start: 0.7211 (ttm-80) cc_final: 0.6558 (mtt-85) REVERT: C 27 ARG cc_start: 0.5220 (mtt90) cc_final: 0.4479 (tmt170) REVERT: H 30 SER cc_start: 0.8563 (p) cc_final: 0.8227 (m) REVERT: H 82 GLN cc_start: 0.7537 (pp30) cc_final: 0.6959 (mm-40) REVERT: H 158 SER cc_start: 0.7303 (p) cc_final: 0.7089 (m) REVERT: H 230 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5701 (ttm) outliers start: 31 outliers final: 20 residues processed: 199 average time/residue: 0.0924 time to fit residues: 25.1251 Evaluate side-chains 186 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 185 VAL 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 155 VAL Chi-restraints excluded: chain H residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.0270 chunk 63 optimal weight: 0.7980 chunk 3 optimal weight: 0.0050 chunk 88 optimal weight: 0.5980 overall best weight: 0.4452 ------------------------------------------------------------------------------- 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** R 167 GLN A 52 GLN B 237 ASN B 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.187942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.145451 restraints weight = 13332.332| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.04 r_work: 0.3784 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8937 Z= 0.103 Angle : 0.560 15.311 12119 Z= 0.277 Chirality : 0.042 0.207 1402 Planarity : 0.003 0.061 1507 Dihedral : 4.467 83.026 1240 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.62 % Allowed : 17.59 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.25), residues: 1108 helix: 1.68 (0.27), residues: 392 sheet: -0.05 (0.31), residues: 265 loop : -1.09 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.021 0.001 TYR A 230 PHE 0.029 0.001 PHE R 182 TRP 0.025 0.001 TRP H 47 HIS 0.002 0.001 HIS R 124 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8936) covalent geometry : angle 0.55981 (12117) SS BOND : bond 0.00125 ( 1) SS BOND : angle 1.37791 ( 2) hydrogen bonds : bond 0.02932 ( 425) hydrogen bonds : angle 3.87097 ( 1194) *********************** 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 217 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.316 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: 0.8247 (m) cc_final: 0.7776 (m) REVERT: R 102 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8156 (tm) REVERT: R 173 ARG cc_start: 0.8260 (mtp-110) cc_final: 0.7840 (mtm110) REVERT: R 197 TYR cc_start: 0.7187 (m-10) cc_final: 0.6586 (m-80) REVERT: A 205 ARG cc_start: 0.6993 (mpp80) cc_final: 0.6749 (mpp80) REVERT: B 105 TYR cc_start: 0.8699 (t80) cc_final: 0.8490 (t80) REVERT: B 179 THR cc_start: 0.8494 (m) cc_final: 0.8272 (p) REVERT: B 220 GLN cc_start: 0.7658 (mt0) cc_final: 0.7318 (mt0) REVERT: B 251 ARG cc_start: 0.7321 (ttm-80) cc_final: 0.6632 (mtt-85) REVERT: C 27 ARG cc_start: 0.5259 (mtt90) cc_final: 0.4539 (tmt170) REVERT: H 30 SER cc_start: 0.8532 (p) cc_final: 0.8210 (m) REVERT: H 230 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5828 (ttm) outliers start: 34 outliers final: 23 residues processed: 200 average time/residue: 0.0828 time to fit residues: 23.0077 Evaluate side-chains 190 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 149 TRP Chi-restraints excluded: chain R residue 150 ASN 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 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 122 SER Chi-restraints excluded: chain B residue 191 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 78 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 237 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** R 167 GLN B 237 ASN B 239 ASN B 295 ASN H 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.183812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.140001 restraints weight = 13455.677| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.07 r_work: 0.3711 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8937 Z= 0.128 Angle : 0.592 15.364 12119 Z= 0.294 Chirality : 0.043 0.312 1402 Planarity : 0.003 0.052 1507 Dihedral : 4.532 79.773 1240 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.58 % Allowed : 18.34 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.26), residues: 1108 helix: 1.69 (0.27), residues: 396 sheet: -0.10 (0.31), residues: 273 loop : -1.01 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 126 TYR 0.015 0.001 TYR R 15 PHE 0.029 0.002 PHE R 182 TRP 0.014 0.001 TRP H 47 HIS 0.009 0.001 HIS R 124 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8936) covalent geometry : angle 0.59179 (12117) SS BOND : bond 0.00136 ( 1) SS BOND : angle 1.31545 ( 2) hydrogen bonds : bond 0.03166 ( 425) hydrogen bonds : angle 3.98441 ( 1194) *********************** 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 219 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.207 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: 0.8333 (m) cc_final: 0.7892 (m) REVERT: R 86 MET cc_start: 0.6340 (ptt) cc_final: 0.5710 (mmt) REVERT: R 102 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8348 (tm) REVERT: R 173 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7778 (mtm110) REVERT: R 197 TYR cc_start: 0.7566 (m-10) cc_final: 0.7123 (m-80) REVERT: A 315 ASP cc_start: 0.8178 (p0) cc_final: 0.7955 (p0) REVERT: B 160 SER cc_start: 0.7951 (m) cc_final: 0.7702 (t) REVERT: B 220 GLN cc_start: 0.7689 (mt0) cc_final: 0.7347 (mt0) REVERT: B 292 PHE cc_start: 0.6368 (m-10) cc_final: 0.6141 (m-10) REVERT: C 27 ARG cc_start: 0.5412 (mtt90) cc_final: 0.4597 (tmt170) REVERT: H 30 SER cc_start: 0.8591 (p) cc_final: 0.8185 (m) REVERT: H 47 TRP cc_start: 0.7287 (t60) cc_final: 0.6984 (t60) outliers start: 43 outliers final: 28 residues processed: 196 average time/residue: 0.0893 time to fit residues: 24.1387 Evaluate side-chains 185 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 89 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 136 LEU 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 185 VAL 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 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 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 237 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 7 optimal weight: 0.1980 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 167 GLN A 52 GLN B 237 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.179150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134322 restraints weight = 12974.660| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 3.01 r_work: 0.3636 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.6333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8937 Z= 0.165 Angle : 0.621 15.213 12119 Z= 0.311 Chirality : 0.043 0.159 1402 Planarity : 0.003 0.049 1507 Dihedral : 4.718 78.039 1240 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.80 % Allowed : 17.27 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.26), residues: 1108 helix: 1.61 (0.27), residues: 397 sheet: -0.14 (0.31), residues: 275 loop : -0.98 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 126 TYR 0.015 0.001 TYR R 15 PHE 0.048 0.002 PHE R 255 TRP 0.013 0.001 TRP R 185 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8936) covalent geometry : angle 0.62126 (12117) SS BOND : bond 0.00319 ( 1) SS BOND : angle 0.84003 ( 2) hydrogen bonds : bond 0.03428 ( 425) hydrogen bonds : angle 4.12125 ( 1194) *********************** 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 217 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8365 (m) cc_final: 0.8092 (m) REVERT: R 58 ASP cc_start: 0.7959 (t0) cc_final: 0.7596 (t70) REVERT: R 86 MET cc_start: 0.6469 (ptt) cc_final: 0.5792 (mmt) REVERT: R 102 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8528 (tm) REVERT: R 173 ARG cc_start: 0.8147 (mtp-110) cc_final: 0.7754 (mtm110) REVERT: R 197 TYR cc_start: 0.7838 (m-10) cc_final: 0.7245 (m-80) REVERT: A 315 ASP cc_start: 0.8328 (p0) cc_final: 0.8093 (p0) REVERT: B 142 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6337 (m90) REVERT: B 220 GLN cc_start: 0.7696 (mt0) cc_final: 0.7364 (mt0) REVERT: B 223 THR cc_start: 0.8335 (p) cc_final: 0.8096 (p) REVERT: B 292 PHE cc_start: 0.7042 (m-10) cc_final: 0.6779 (m-10) REVERT: C 27 ARG cc_start: 0.5683 (mtt90) cc_final: 0.4707 (tmt170) REVERT: H 30 SER cc_start: 0.8775 (p) cc_final: 0.8392 (m) REVERT: H 47 TRP cc_start: 0.7461 (t60) cc_final: 0.7227 (t60) outliers start: 45 outliers final: 27 residues processed: 197 average time/residue: 0.0787 time to fit residues: 21.7550 Evaluate side-chains 184 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 242 SER 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 185 VAL Chi-restraints excluded: chain A residue 224 CYS 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 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 124 HIS R 167 GLN A 52 GLN A 311 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.179538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.138171 restraints weight = 13170.548| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.96 r_work: 0.3659 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8937 Z= 0.128 Angle : 0.613 15.395 12119 Z= 0.301 Chirality : 0.042 0.181 1402 Planarity : 0.003 0.050 1507 Dihedral : 4.619 76.461 1240 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.48 % Allowed : 18.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.26), residues: 1108 helix: 1.68 (0.27), residues: 397 sheet: -0.14 (0.31), residues: 275 loop : -0.91 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 126 TYR 0.016 0.001 TYR R 265 PHE 0.033 0.002 PHE R 182 TRP 0.018 0.001 TRP R 185 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8936) covalent geometry : angle 0.61338 (12117) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.75338 ( 2) hydrogen bonds : bond 0.03231 ( 425) hydrogen bonds : angle 4.07003 ( 1194) *********************** 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 201 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.321 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: 0.8388 (m) cc_final: 0.8072 (m) REVERT: R 58 ASP cc_start: 0.7962 (t0) cc_final: 0.7674 (t70) REVERT: R 86 MET cc_start: 0.6371 (ptt) cc_final: 0.5725 (mmt) REVERT: R 173 ARG cc_start: 0.8122 (mtp-110) cc_final: 0.7690 (mtm110) REVERT: R 197 TYR cc_start: 0.7865 (m-10) cc_final: 0.7264 (m-80) REVERT: A 315 ASP cc_start: 0.8357 (p0) cc_final: 0.8117 (p0) REVERT: B 129 ARG cc_start: 0.8177 (ttt90) cc_final: 0.7703 (ttm110) REVERT: B 220 GLN cc_start: 0.7618 (mt0) cc_final: 0.7298 (mt0) REVERT: B 223 THR cc_start: 0.8291 (p) cc_final: 0.8074 (p) REVERT: B 292 PHE cc_start: 0.6998 (m-10) cc_final: 0.6743 (m-10) REVERT: C 27 ARG cc_start: 0.5677 (mtt90) cc_final: 0.4741 (tmt170) REVERT: H 27 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6632 (p90) REVERT: H 30 SER cc_start: 0.8784 (p) cc_final: 0.8386 (m) outliers start: 42 outliers final: 31 residues processed: 185 average time/residue: 0.0827 time to fit residues: 21.6657 Evaluate side-chains 185 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 127 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 262 LEU Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP 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 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 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 0.0050 chunk 42 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.0170 chunk 15 optimal weight: 5.9990 overall best weight: 2.0038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 124 HIS ** R 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.174252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.128526 restraints weight = 12942.730| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.98 r_work: 0.3560 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8937 Z= 0.199 Angle : 0.689 15.180 12119 Z= 0.342 Chirality : 0.046 0.200 1402 Planarity : 0.003 0.029 1507 Dihedral : 4.902 73.681 1240 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.26 % Allowed : 18.98 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.25), residues: 1108 helix: 1.56 (0.27), residues: 397 sheet: -0.13 (0.33), residues: 249 loop : -1.01 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 125 TYR 0.015 0.002 TYR B 105 PHE 0.037 0.002 PHE R 182 TRP 0.041 0.002 TRP H 47 HIS 0.011 0.002 HIS R 124 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 8936) covalent geometry : angle 0.68861 (12117) SS BOND : bond 0.00469 ( 1) SS BOND : angle 1.39433 ( 2) hydrogen bonds : bond 0.03783 ( 425) hydrogen bonds : angle 4.31408 ( 1194) *********************** 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 217 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8535 (m) cc_final: 0.8246 (m) REVERT: R 58 ASP cc_start: 0.7961 (t0) cc_final: 0.7683 (t70) REVERT: R 86 MET cc_start: 0.6534 (ptt) cc_final: 0.5803 (mmt) REVERT: R 173 ARG cc_start: 0.8204 (mtp-110) cc_final: 0.7945 (mtp-110) REVERT: R 197 TYR cc_start: 0.8056 (m-10) cc_final: 0.7551 (m-80) REVERT: A 247 MET cc_start: 0.7180 (ptt) cc_final: 0.6900 (ptm) REVERT: A 315 ASP cc_start: 0.8611 (p0) cc_final: 0.8365 (p0) REVERT: B 45 MET cc_start: 0.8067 (tpp) cc_final: 0.7852 (mmm) REVERT: B 129 ARG cc_start: 0.8243 (ttt90) cc_final: 0.7815 (ttm110) REVERT: B 142 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7330 (m90) REVERT: B 220 GLN cc_start: 0.7666 (mt0) cc_final: 0.7353 (mt0) REVERT: C 27 ARG cc_start: 0.5924 (mtt90) cc_final: 0.4718 (tmt170) REVERT: H 27 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7236 (p90) REVERT: H 30 SER cc_start: 0.8902 (p) cc_final: 0.8533 (m) REVERT: H 233 LEU cc_start: 0.8743 (tp) cc_final: 0.8527 (tp) outliers start: 40 outliers final: 33 residues processed: 200 average time/residue: 0.0911 time to fit residues: 24.9374 Evaluate side-chains 193 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 127 ILE 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 185 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 71 VAL 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 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 27 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 237 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 0.0040 chunk 43 optimal weight: 10.0000 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 124 HIS ** R 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 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 = 0.4254 r_free = 0.4254 target = 0.176386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131315 restraints weight = 12763.798| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.99 r_work: 0.3598 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.7585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8937 Z= 0.137 Angle : 0.657 15.183 12119 Z= 0.323 Chirality : 0.044 0.227 1402 Planarity : 0.004 0.043 1507 Dihedral : 4.753 71.995 1240 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.05 % Allowed : 19.94 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.26), residues: 1108 helix: 1.71 (0.27), residues: 396 sheet: -0.23 (0.32), residues: 260 loop : -0.96 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 24 TYR 0.016 0.001 TYR R 15 PHE 0.035 0.002 PHE H 239 TRP 0.060 0.002 TRP H 47 HIS 0.004 0.001 HIS R 124 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8936) covalent geometry : angle 0.65648 (12117) SS BOND : bond 0.00261 ( 1) SS BOND : angle 1.02011 ( 2) hydrogen bonds : bond 0.03519 ( 425) hydrogen bonds : angle 4.29719 ( 1194) *********************** 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 194 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8433 (m) cc_final: 0.8163 (m) REVERT: R 58 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7588 (t70) REVERT: R 86 MET cc_start: 0.6539 (ptt) cc_final: 0.5813 (mmt) REVERT: R 173 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7771 (mtm110) REVERT: R 197 TYR cc_start: 0.8069 (m-10) cc_final: 0.7566 (m-80) REVERT: A 247 MET cc_start: 0.7152 (ptt) cc_final: 0.6892 (ptm) REVERT: A 315 ASP cc_start: 0.8660 (p0) cc_final: 0.8352 (p0) REVERT: B 45 MET cc_start: 0.7899 (tpp) cc_final: 0.7662 (mmm) REVERT: B 129 ARG cc_start: 0.8247 (ttt90) cc_final: 0.7822 (ttm110) REVERT: B 220 GLN cc_start: 0.7673 (mt0) cc_final: 0.7354 (mt0) REVERT: C 27 ARG cc_start: 0.5958 (mtt90) cc_final: 0.4749 (tmt170) REVERT: H 27 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.7141 (p90) REVERT: H 30 SER cc_start: 0.8872 (p) cc_final: 0.8532 (m) REVERT: H 233 LEU cc_start: 0.8787 (tp) cc_final: 0.8417 (tp) outliers start: 38 outliers final: 32 residues processed: 179 average time/residue: 0.0845 time to fit residues: 21.0627 Evaluate side-chains 186 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 58 ASP Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 242 SER 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 185 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 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 45 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 237 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 167 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 = 0.4251 r_free = 0.4251 target = 0.176318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131402 restraints weight = 12860.988| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.97 r_work: 0.3602 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.7741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8937 Z= 0.136 Angle : 0.656 15.186 12119 Z= 0.321 Chirality : 0.044 0.165 1402 Planarity : 0.003 0.041 1507 Dihedral : 4.666 70.247 1240 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.41 % Allowed : 20.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.26), residues: 1108 helix: 1.74 (0.28), residues: 397 sheet: -0.11 (0.32), residues: 251 loop : -0.99 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 24 TYR 0.016 0.001 TYR A 296 PHE 0.036 0.002 PHE R 182 TRP 0.043 0.002 TRP H 47 HIS 0.003 0.001 HIS H 232 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8936) covalent geometry : angle 0.65559 (12117) SS BOND : bond 0.00249 ( 1) SS BOND : angle 1.01014 ( 2) hydrogen bonds : bond 0.03450 ( 425) hydrogen bonds : angle 4.26511 ( 1194) ********************** 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 186 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 CYS cc_start: 0.8511 (m) cc_final: 0.8235 (m) REVERT: R 58 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7617 (t70) REVERT: R 86 MET cc_start: 0.6528 (ptt) cc_final: 0.5849 (mmt) REVERT: R 173 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7830 (mtm110) REVERT: R 197 TYR cc_start: 0.8070 (m-10) cc_final: 0.7556 (m-80) REVERT: A 247 MET cc_start: 0.7234 (ptt) cc_final: 0.6969 (ptm) REVERT: A 315 ASP cc_start: 0.8654 (p0) cc_final: 0.8353 (p0) REVERT: B 45 MET cc_start: 0.7782 (tpp) cc_final: 0.7563 (mmm) REVERT: B 129 ARG cc_start: 0.8265 (ttt90) cc_final: 0.7868 (ttm110) REVERT: B 220 GLN cc_start: 0.7683 (mt0) cc_final: 0.7364 (mt0) REVERT: C 27 ARG cc_start: 0.6076 (mtt90) cc_final: 0.4775 (tmt170) REVERT: H 30 SER cc_start: 0.8879 (p) cc_final: 0.8522 (m) REVERT: H 230 MET cc_start: 0.7404 (tpp) cc_final: 0.6522 (tpp) REVERT: H 233 LEU cc_start: 0.8793 (tp) cc_final: 0.8468 (tp) outliers start: 32 outliers final: 28 residues processed: 172 average time/residue: 0.0871 time to fit residues: 20.8185 Evaluate side-chains 178 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 58 ASP Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 124 HIS Chi-restraints excluded: chain R residue 127 ILE Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 242 SER 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 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 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 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 117 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 1 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 167 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 = 0.4239 r_free = 0.4239 target = 0.175128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129902 restraints weight = 13108.948| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.98 r_work: 0.3578 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.7928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8937 Z= 0.154 Angle : 0.666 14.882 12119 Z= 0.327 Chirality : 0.044 0.196 1402 Planarity : 0.003 0.039 1507 Dihedral : 4.725 69.910 1240 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.52 % Allowed : 20.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.25), residues: 1108 helix: 1.74 (0.27), residues: 394 sheet: -0.09 (0.33), residues: 245 loop : -0.99 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 125 TYR 0.014 0.001 TYR R 15 PHE 0.036 0.002 PHE R 182 TRP 0.047 0.002 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8936) covalent geometry : angle 0.66549 (12117) SS BOND : bond 0.00268 ( 1) SS BOND : angle 1.03707 ( 2) hydrogen bonds : bond 0.03544 ( 425) hydrogen bonds : angle 4.29713 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2233.82 seconds wall clock time: 39 minutes 2.72 seconds (2342.72 seconds total)