Starting phenix.real_space_refine on Thu Jul 2 14:10:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8j_34549/07_2026/8h8j_34549_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8j_34549/07_2026/8h8j_34549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h8j_34549/07_2026/8h8j_34549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8j_34549/07_2026/8h8j_34549.map" model { file = "/net/cci-nas-00/data/ceres_data/8h8j_34549/07_2026/8h8j_34549_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8j_34549/07_2026/8h8j_34549_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 63 5.16 5 Cl 1 4.86 5 C 5648 2.51 5 N 1511 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1842 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2553 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 2191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2191 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 271} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 417 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1733 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CLR': 3, 'WYB': 1} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 1 Time building chain proxies: 1.60, per 1000 atoms: 0.18 Number of scatterers: 8842 At special positions: 0 Unit cell: (105.04, 113.36, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 Cl 1 17.00 S 63 16.00 O 1618 8.00 N 1511 7.00 C 5648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 89 " - pdb=" SG CYS C 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 332.1 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 36.1% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 48 removed outlier: 3.655A pdb=" N THR A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 73 removed outlier: 3.815A pdb=" N ILE A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.663A pdb=" N PHE A 238 " --> pdb=" O PHE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.898A pdb=" N GLN A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 335 removed outlier: 3.665A pdb=" N ARG A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 375 removed outlier: 3.619A pdb=" N LEU A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 16 through 45 removed outlier: 4.136A pdb=" N LEU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 79 Proline residue: C 74 - end of helix Processing helix chain 'C' and resid 86 through 119 Processing helix chain 'C' and resid 121 through 125 removed outlier: 3.613A pdb=" N ARG C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 158 removed outlier: 3.535A pdb=" N GLN C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 removed outlier: 3.657A pdb=" N LEU C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 198 Processing helix chain 'C' and resid 205 through 241 Proline residue: C 232 - end of helix removed outlier: 3.869A pdb=" N LEU C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 267 removed outlier: 3.983A pdb=" N THR C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C 263 " --> pdb=" O TYR C 259 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 280 through 288 removed outlier: 3.642A pdb=" N GLN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 4.575A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.171A pdb=" N VAL A 49 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL A 222 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 51 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS A 50 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU A 245 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A 52 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU A 247 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 54 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N SER A 249 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.870A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.712A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.799A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.637A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.045A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.896A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.393A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.803A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.275A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 4.359A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1242 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: 0.92 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1416 1.27 - 1.41: 2239 1.41 - 1.54: 5262 1.54 - 1.68: 17 1.68 - 1.81: 90 Bond restraints: 9024 Sorted by residual: bond pdb=" C02 WYB C 401 " pdb=" C03 WYB C 401 " ideal model delta sigma weight residual 1.427 1.528 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C07 WYB C 401 " pdb=" N06 WYB C 401 " ideal model delta sigma weight residual 1.361 1.450 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C16 WYB C 401 " pdb=" N15 WYB C 401 " ideal model delta sigma weight residual 1.363 1.447 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C12 WYB C 401 " pdb="CL13 WYB C 401 " ideal model delta sigma weight residual 1.727 1.781 -0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" CA THR C 166 " pdb=" C THR C 166 " ideal model delta sigma weight residual 1.527 1.489 0.038 1.42e-02 4.96e+03 7.11e+00 ... (remaining 9019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 12037 2.07 - 4.14: 179 4.14 - 6.21: 33 6.21 - 8.27: 11 8.27 - 10.34: 5 Bond angle restraints: 12265 Sorted by residual: angle pdb=" N HIS C 168 " pdb=" CA HIS C 168 " pdb=" C HIS C 168 " ideal model delta sigma weight residual 108.63 98.29 10.34 1.60e+00 3.91e-01 4.18e+01 angle pdb=" N ASN C 169 " pdb=" CA ASN C 169 " pdb=" C ASN C 169 " ideal model delta sigma weight residual 110.33 118.02 -7.69 1.29e+00 6.01e-01 3.55e+01 angle pdb=" N ASN C 171 " pdb=" CA ASN C 171 " pdb=" C ASN C 171 " ideal model delta sigma weight residual 114.75 108.38 6.37 1.26e+00 6.30e-01 2.56e+01 angle pdb=" N SER C 172 " pdb=" CA SER C 172 " pdb=" C SER C 172 " ideal model delta sigma weight residual 112.45 106.03 6.42 1.39e+00 5.18e-01 2.13e+01 angle pdb=" C THR C 83 " pdb=" N SER C 84 " pdb=" CA SER C 84 " ideal model delta sigma weight residual 121.90 116.43 5.47 1.26e+00 6.30e-01 1.89e+01 ... (remaining 12260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5220 17.56 - 35.12: 202 35.12 - 52.68: 51 52.68 - 70.25: 14 70.25 - 87.81: 2 Dihedral angle restraints: 5489 sinusoidal: 2188 harmonic: 3301 Sorted by residual: dihedral pdb=" CB CYS C 89 " pdb=" SG CYS C 89 " pdb=" SG CYS C 162 " pdb=" CB CYS C 162 " ideal model delta sinusoidal sigma weight residual -86.00 -144.27 58.27 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CA ASP C 82 " pdb=" CB ASP C 82 " pdb=" CG ASP C 82 " pdb=" OD1 ASP C 82 " ideal model delta sinusoidal sigma weight residual -30.00 -85.76 55.76 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA MET C 173 " pdb=" CB MET C 173 " pdb=" CG MET C 173 " pdb=" SD MET C 173 " ideal model delta sinusoidal sigma weight residual -180.00 -120.13 -59.87 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1172 0.048 - 0.096: 190 0.096 - 0.144: 52 0.144 - 0.192: 5 0.192 - 0.240: 6 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CA ASN C 169 " pdb=" N ASN C 169 " pdb=" C ASN C 169 " pdb=" CB ASN C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C13 CLR C 404 " pdb=" C12 CLR C 404 " pdb=" C14 CLR C 404 " pdb=" C17 CLR C 404 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C13 CLR C 405 " pdb=" C12 CLR C 405 " pdb=" C14 CLR C 405 " pdb=" C17 CLR C 405 " both_signs ideal model delta sigma weight residual False -2.93 -2.71 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1422 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO B 236 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 335 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C ARG A 335 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG A 335 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 336 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 217 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 218 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " -0.023 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 57 2.53 - 3.12: 6660 3.12 - 3.72: 14019 3.72 - 4.31: 19564 4.31 - 4.90: 32854 Nonbonded interactions: 73154 Sorted by model distance: nonbonded pdb=" O ARG A 332 " pdb=" NE2 GLN A 338 " model vdw 1.939 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR H 175 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.186 3.040 nonbonded pdb=" O ARG A 335 " pdb=" OE1 GLN A 338 " model vdw 2.200 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.210 3.040 ... (remaining 73149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.530 Find NCS groups from input model: 0.030 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 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 : 0.003 0.101 9025 Z= 0.198 Angle : 0.664 10.343 12267 Z= 0.373 Chirality : 0.042 0.240 1425 Planarity : 0.003 0.050 1536 Dihedral : 10.436 87.807 3354 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.32 % Favored : 97.60 % Rotamer: Outliers : 2.59 % Allowed : 4.85 % Favored : 92.56 % 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 are not related in a simple way. whole: -0.78 (0.24), residues: 1123 helix: 0.76 (0.25), residues: 393 sheet: -0.54 (0.29), residues: 264 loop : -1.58 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.006 0.001 TYR C 101 PHE 0.008 0.001 PHE B 199 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.000 HIS C 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.20 ( 9024) covalent geometry : angle 0.66445 / 0.37 (12265) SS BOND : bond 0.00246 / 0.13 ( 1) SS BOND : angle 0.80765 / 0.46 ( 2) hydrogen bonds : bond 0.11809 / 8.10 ( 433) hydrogen bonds : angle 4.60156 / 3.18 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 0.207 Fit side-chains REVERT: A 10 LYS cc_start: 0.7610 (mtmm) cc_final: 0.7407 (mtmm) REVERT: A 16 SER cc_start: 0.7617 (t) cc_final: 0.7404 (t) REVERT: A 51 ILE cc_start: 0.8363 (mm) cc_final: 0.8133 (mt) REVERT: A 244 ILE cc_start: 0.7530 (pt) cc_final: 0.7105 (mt) REVERT: A 250 SER cc_start: 0.7413 (m) cc_final: 0.7205 (m) REVERT: A 270 LEU cc_start: 0.8126 (mm) cc_final: 0.7849 (mp) REVERT: A 299 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6429 (mm-30) REVERT: B 25 CYS cc_start: 0.7140 (m) cc_final: 0.6864 (m) REVERT: B 83 ASP cc_start: 0.7790 (t0) cc_final: 0.7557 (t0) REVERT: B 117 LEU cc_start: 0.7596 (mt) cc_final: 0.7361 (mt) REVERT: B 124 TYR cc_start: 0.8041 (m-80) cc_final: 0.7512 (m-80) REVERT: B 271 CYS cc_start: 0.7444 (p) cc_final: 0.7168 (p) REVERT: B 289 TYR cc_start: 0.8075 (m-80) cc_final: 0.7071 (m-80) REVERT: B 295 ASN cc_start: 0.7722 (m-40) cc_final: 0.7438 (m110) REVERT: B 297 TRP cc_start: 0.7838 (m100) cc_final: 0.7451 (m100) REVERT: B 303 ASP cc_start: 0.7004 (p0) cc_final: 0.6734 (p0) REVERT: B 333 ASP cc_start: 0.7024 (p0) cc_final: 0.6749 (p0) REVERT: C 90 GLN cc_start: 0.7743 (mt0) cc_final: 0.7486 (mt0) REVERT: C 102 MET cc_start: 0.6621 (tpt) cc_final: 0.6246 (tpt) REVERT: C 123 ARG cc_start: 0.7039 (mtt-85) cc_final: 0.6825 (mtt-85) REVERT: G 44 HIS cc_start: 0.8144 (m90) cc_final: 0.7894 (m90) REVERT: H 90 ASP cc_start: 0.7392 (m-30) cc_final: 0.7153 (m-30) REVERT: H 156 SER cc_start: 0.7551 (m) cc_final: 0.7296 (t) outliers start: 24 outliers final: 11 residues processed: 269 average time/residue: 0.0832 time to fit residues: 30.6834 Evaluate side-chains 230 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 219 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 263 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0030 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN A 339 GLN A 340 GLN B 176 GLN B 220 GLN B 237 ASN C 99 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.126243 restraints weight = 12471.608| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.91 r_work: 0.3540 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9025 Z= 0.146 Angle : 0.537 8.358 12267 Z= 0.277 Chirality : 0.040 0.136 1425 Planarity : 0.004 0.049 1536 Dihedral : 7.372 85.467 1461 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.24 % Allowed : 12.51 % Favored : 84.25 % 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 are not related in a simple way. whole: 0.25 (0.26), residues: 1123 helix: 1.81 (0.27), residues: 393 sheet: -0.25 (0.28), residues: 280 loop : -1.00 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 56 TYR 0.018 0.002 TYR H 190 PHE 0.019 0.002 PHE A 212 TRP 0.017 0.002 TRP B 169 HIS 0.007 0.001 HIS H 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 9024) covalent geometry : angle 0.53732 / 0.28 (12265) SS BOND : bond 0.00063 / 0.03 ( 1) SS BOND : angle 0.48146 / 0.22 ( 2) hydrogen bonds : bond 0.03105 / 2.12 ( 433) hydrogen bonds : angle 3.79602 / 2.69 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.199 Fit side-chains REVERT: A 10 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7704 (mtmm) REVERT: B 25 CYS cc_start: 0.7864 (m) cc_final: 0.7540 (m) REVERT: B 32 GLN cc_start: 0.7532 (mt0) cc_final: 0.7113 (mt0) REVERT: B 134 ARG cc_start: 0.8200 (mtm110) cc_final: 0.7832 (mtm110) REVERT: B 249 THR cc_start: 0.7873 (p) cc_final: 0.7626 (t) REVERT: B 297 TRP cc_start: 0.8425 (m100) cc_final: 0.8149 (m100) REVERT: B 303 ASP cc_start: 0.7553 (p0) cc_final: 0.7180 (p0) REVERT: B 336 LEU cc_start: 0.8171 (mt) cc_final: 0.7740 (mp) REVERT: B 340 ASN cc_start: 0.7444 (m110) cc_final: 0.7133 (t0) REVERT: C 90 GLN cc_start: 0.8215 (mt0) cc_final: 0.7956 (mt0) REVERT: C 102 MET cc_start: 0.7433 (tpt) cc_final: 0.6969 (tpt) REVERT: C 123 ARG cc_start: 0.7847 (mtt-85) cc_final: 0.7631 (mtt-85) REVERT: G 21 MET cc_start: 0.8169 (tmm) cc_final: 0.7940 (tmm) REVERT: G 44 HIS cc_start: 0.8403 (m90) cc_final: 0.8168 (m90) outliers start: 30 outliers final: 16 residues processed: 238 average time/residue: 0.0805 time to fit residues: 26.3887 Evaluate side-chains 215 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 186 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 93 optimal weight: 0.0020 chunk 48 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 0.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.144569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.129563 restraints weight = 12227.968| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.04 r_work: 0.3501 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9025 Z= 0.123 Angle : 0.509 7.117 12267 Z= 0.262 Chirality : 0.039 0.135 1425 Planarity : 0.004 0.051 1536 Dihedral : 5.871 58.108 1447 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.78 % Allowed : 14.46 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 1123 helix: 2.06 (0.27), residues: 390 sheet: 0.09 (0.29), residues: 280 loop : -0.89 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 164 TYR 0.014 0.001 TYR H 190 PHE 0.023 0.001 PHE H 29 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 9024) covalent geometry : angle 0.50867 / 0.26 (12265) SS BOND : bond 0.00084 / 0.04 ( 1) SS BOND : angle 0.61726 / 0.31 ( 2) hydrogen bonds : bond 0.02964 / 2.00 ( 433) hydrogen bonds : angle 3.73543 / 2.66 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.208 Fit side-chains REVERT: A 10 LYS cc_start: 0.8034 (mtmm) cc_final: 0.7736 (mtmm) REVERT: A 51 ILE cc_start: 0.8739 (mm) cc_final: 0.8498 (mt) REVERT: A 217 VAL cc_start: 0.8566 (p) cc_final: 0.8223 (m) REVERT: B 32 GLN cc_start: 0.7565 (mt0) cc_final: 0.7282 (mt0) REVERT: B 59 TYR cc_start: 0.8361 (m-80) cc_final: 0.8109 (m-80) REVERT: B 75 GLN cc_start: 0.6859 (mt0) cc_final: 0.6564 (mt0) REVERT: B 134 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7847 (mtm110) REVERT: B 249 THR cc_start: 0.7956 (p) cc_final: 0.7731 (t) REVERT: B 303 ASP cc_start: 0.7662 (p0) cc_final: 0.7287 (p0) REVERT: B 325 MET cc_start: 0.8090 (tpp) cc_final: 0.7737 (tpp) REVERT: B 331 SER cc_start: 0.8393 (p) cc_final: 0.7973 (p) REVERT: C 21 LEU cc_start: 0.7637 (tp) cc_final: 0.7369 (tp) REVERT: C 90 GLN cc_start: 0.8288 (mt0) cc_final: 0.7994 (mt0) REVERT: C 102 MET cc_start: 0.7446 (tpt) cc_final: 0.6947 (tpt) REVERT: C 123 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.7654 (mtt-85) REVERT: C 279 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.7006 (mtm) REVERT: H 32 PHE cc_start: 0.8548 (m-80) cc_final: 0.8117 (m-80) outliers start: 35 outliers final: 18 residues processed: 233 average time/residue: 0.0749 time to fit residues: 24.0344 Evaluate side-chains 230 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 186 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN C 6 ASN C 171 ASN H 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118603 restraints weight = 12478.298| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.05 r_work: 0.3416 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9025 Z= 0.238 Angle : 0.593 8.174 12267 Z= 0.307 Chirality : 0.043 0.147 1425 Planarity : 0.004 0.050 1536 Dihedral : 5.979 57.602 1447 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.10 % Allowed : 16.40 % Favored : 79.50 % 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 are not related in a simple way. whole: 0.47 (0.26), residues: 1123 helix: 1.82 (0.27), residues: 392 sheet: 0.02 (0.29), residues: 280 loop : -0.81 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 125 TYR 0.022 0.002 TYR H 59 PHE 0.022 0.002 PHE B 235 TRP 0.017 0.002 TRP B 169 HIS 0.006 0.002 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.24 ( 9024) covalent geometry : angle 0.59299 / 0.31 (12265) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 0.61340 / 0.30 ( 2) hydrogen bonds : bond 0.03582 / 2.38 ( 433) hydrogen bonds : angle 4.14668 / 2.95 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7907 (mtmm) REVERT: A 54 LEU cc_start: 0.8384 (mt) cc_final: 0.8183 (mp) REVERT: A 364 LYS cc_start: 0.8380 (ttpp) cc_final: 0.8174 (ttpt) REVERT: B 32 GLN cc_start: 0.7884 (mt0) cc_final: 0.7475 (mt0) REVERT: B 74 SER cc_start: 0.8739 (t) cc_final: 0.8223 (p) REVERT: B 134 ARG cc_start: 0.8196 (mtm110) cc_final: 0.7809 (mtm110) REVERT: B 262 MET cc_start: 0.7465 (mmm) cc_final: 0.7209 (mmm) REVERT: B 303 ASP cc_start: 0.7814 (p0) cc_final: 0.7378 (p0) REVERT: B 336 LEU cc_start: 0.8254 (mt) cc_final: 0.7805 (mp) REVERT: C 21 LEU cc_start: 0.7818 (tp) cc_final: 0.7531 (tp) REVERT: C 53 THR cc_start: 0.7656 (t) cc_final: 0.7134 (p) REVERT: C 56 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7532 (ttt-90) REVERT: C 64 VAL cc_start: 0.7959 (t) cc_final: 0.7704 (p) REVERT: C 90 GLN cc_start: 0.8337 (mt0) cc_final: 0.7996 (mt0) REVERT: C 102 MET cc_start: 0.7529 (tpt) cc_final: 0.7017 (tpt) REVERT: G 32 LYS cc_start: 0.8455 (ttpp) cc_final: 0.8194 (ttpp) REVERT: H 103 TYR cc_start: 0.8595 (t80) cc_final: 0.8030 (t80) REVERT: H 155 VAL cc_start: 0.8219 (p) cc_final: 0.7968 (m) outliers start: 38 outliers final: 28 residues processed: 238 average time/residue: 0.0776 time to fit residues: 25.3157 Evaluate side-chains 231 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 chunk 55 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 230 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119980 restraints weight = 12348.212| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.04 r_work: 0.3415 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9025 Z= 0.158 Angle : 0.552 6.551 12267 Z= 0.285 Chirality : 0.041 0.146 1425 Planarity : 0.004 0.048 1536 Dihedral : 5.825 59.938 1447 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.78 % Allowed : 18.23 % Favored : 77.99 % 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 are not related in a simple way. whole: 0.58 (0.26), residues: 1123 helix: 2.03 (0.27), residues: 389 sheet: -0.03 (0.28), residues: 290 loop : -0.78 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 100 TYR 0.021 0.002 TYR H 50 PHE 0.030 0.002 PHE H 239 TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 9024) covalent geometry : angle 0.55147 / 0.29 (12265) SS BOND : bond 0.00082 / 0.04 ( 1) SS BOND : angle 0.79370 / 0.38 ( 2) hydrogen bonds : bond 0.03253 / 2.18 ( 433) hydrogen bonds : angle 4.10056 / 2.92 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8212 (mtmm) cc_final: 0.7929 (mtmm) REVERT: A 217 VAL cc_start: 0.8655 (p) cc_final: 0.8363 (m) REVERT: B 32 GLN cc_start: 0.7879 (mt0) cc_final: 0.7464 (mt0) REVERT: B 74 SER cc_start: 0.8750 (t) cc_final: 0.8245 (p) REVERT: B 134 ARG cc_start: 0.8283 (mtm110) cc_final: 0.7905 (mtm110) REVERT: B 243 THR cc_start: 0.7501 (p) cc_final: 0.7296 (p) REVERT: B 303 ASP cc_start: 0.7801 (p0) cc_final: 0.7378 (p0) REVERT: C 21 LEU cc_start: 0.7772 (tp) cc_final: 0.7491 (tp) REVERT: C 53 THR cc_start: 0.7651 (t) cc_final: 0.7141 (p) REVERT: C 90 GLN cc_start: 0.8339 (mt0) cc_final: 0.7990 (mt0) REVERT: C 102 MET cc_start: 0.7537 (tpt) cc_final: 0.6999 (tpt) REVERT: H 32 PHE cc_start: 0.8598 (m-80) cc_final: 0.8091 (m-80) REVERT: H 103 TYR cc_start: 0.8571 (t80) cc_final: 0.8004 (t80) REVERT: H 155 VAL cc_start: 0.8236 (p) cc_final: 0.7997 (m) outliers start: 35 outliers final: 30 residues processed: 234 average time/residue: 0.0794 time to fit residues: 25.3382 Evaluate side-chains 226 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN B 230 ASN B 340 ASN C 38 ASN C 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119157 restraints weight = 12366.810| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.03 r_work: 0.3420 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9025 Z= 0.171 Angle : 0.560 6.644 12267 Z= 0.289 Chirality : 0.042 0.146 1425 Planarity : 0.004 0.046 1536 Dihedral : 5.788 58.058 1447 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.99 % Allowed : 18.02 % Favored : 77.99 % 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 are not related in a simple way. whole: 0.61 (0.26), residues: 1123 helix: 2.01 (0.27), residues: 392 sheet: -0.03 (0.28), residues: 289 loop : -0.71 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 164 TYR 0.019 0.002 TYR H 50 PHE 0.024 0.002 PHE C 163 TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 9024) covalent geometry : angle 0.55978 / 0.29 (12265) SS BOND : bond 0.00047 / 0.02 ( 1) SS BOND : angle 0.94369 / 0.46 ( 2) hydrogen bonds : bond 0.03325 / 2.22 ( 433) hydrogen bonds : angle 4.14259 / 2.96 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7912 (mtmm) REVERT: A 217 VAL cc_start: 0.8653 (p) cc_final: 0.8365 (m) REVERT: B 32 GLN cc_start: 0.7774 (mt0) cc_final: 0.7370 (mt0) REVERT: B 74 SER cc_start: 0.8713 (t) cc_final: 0.8181 (p) REVERT: B 134 ARG cc_start: 0.8258 (mtm110) cc_final: 0.7871 (mtm110) REVERT: B 161 SER cc_start: 0.8215 (p) cc_final: 0.7885 (p) REVERT: B 165 THR cc_start: 0.7977 (p) cc_final: 0.7078 (m) REVERT: B 243 THR cc_start: 0.7414 (p) cc_final: 0.7180 (p) REVERT: B 262 MET cc_start: 0.7470 (mmm) cc_final: 0.7076 (mmm) REVERT: C 21 LEU cc_start: 0.7789 (tp) cc_final: 0.7508 (tp) REVERT: C 53 THR cc_start: 0.7614 (t) cc_final: 0.7100 (p) REVERT: C 90 GLN cc_start: 0.8352 (mt0) cc_final: 0.7954 (mt0) REVERT: C 102 MET cc_start: 0.7513 (tpt) cc_final: 0.6985 (tpt) REVERT: H 32 PHE cc_start: 0.8587 (m-80) cc_final: 0.8070 (m-80) REVERT: H 103 TYR cc_start: 0.8577 (t80) cc_final: 0.7994 (t80) REVERT: H 155 VAL cc_start: 0.8222 (p) cc_final: 0.7979 (m) outliers start: 37 outliers final: 33 residues processed: 225 average time/residue: 0.0901 time to fit residues: 27.5495 Evaluate side-chains 232 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 20 optimal weight: 0.0270 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN B 230 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122052 restraints weight = 12379.523| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.93 r_work: 0.3475 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9025 Z= 0.128 Angle : 0.545 6.957 12267 Z= 0.280 Chirality : 0.040 0.143 1425 Planarity : 0.004 0.046 1536 Dihedral : 5.660 56.504 1447 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.88 % Allowed : 18.77 % Favored : 77.35 % 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 are not related in a simple way. whole: 0.71 (0.26), residues: 1123 helix: 2.08 (0.27), residues: 393 sheet: -0.01 (0.28), residues: 289 loop : -0.61 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 123 TYR 0.017 0.001 TYR H 50 PHE 0.020 0.001 PHE H 239 TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9024) covalent geometry : angle 0.54462 / 0.28 (12265) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 0.99298 / 0.47 ( 2) hydrogen bonds : bond 0.03136 / 2.09 ( 433) hydrogen bonds : angle 4.06809 / 2.90 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7931 (mtmm) REVERT: A 217 VAL cc_start: 0.8670 (p) cc_final: 0.8385 (m) REVERT: B 32 GLN cc_start: 0.7769 (mt0) cc_final: 0.7370 (mt0) REVERT: B 74 SER cc_start: 0.8695 (t) cc_final: 0.8099 (p) REVERT: B 134 ARG cc_start: 0.8263 (mtm110) cc_final: 0.7917 (mtm110) REVERT: B 243 THR cc_start: 0.7297 (p) cc_final: 0.7087 (p) REVERT: B 262 MET cc_start: 0.7228 (mmm) cc_final: 0.6949 (mmm) REVERT: B 303 ASP cc_start: 0.7771 (p0) cc_final: 0.7438 (p0) REVERT: C 21 LEU cc_start: 0.7733 (tp) cc_final: 0.7457 (tp) REVERT: C 53 THR cc_start: 0.7686 (t) cc_final: 0.7186 (p) REVERT: C 90 GLN cc_start: 0.8340 (mt0) cc_final: 0.7971 (mt0) REVERT: C 102 MET cc_start: 0.7541 (tpt) cc_final: 0.7022 (tpt) REVERT: G 32 LYS cc_start: 0.8543 (ttpp) cc_final: 0.8301 (ttpp) REVERT: H 32 PHE cc_start: 0.8603 (m-80) cc_final: 0.8137 (m-80) REVERT: H 103 TYR cc_start: 0.8520 (t80) cc_final: 0.7934 (t80) REVERT: H 155 VAL cc_start: 0.8242 (p) cc_final: 0.8034 (m) outliers start: 36 outliers final: 32 residues processed: 217 average time/residue: 0.0849 time to fit residues: 24.9832 Evaluate side-chains 219 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 246 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN B 230 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120719 restraints weight = 12318.233| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.93 r_work: 0.3456 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9025 Z= 0.178 Angle : 0.563 8.106 12267 Z= 0.291 Chirality : 0.042 0.152 1425 Planarity : 0.004 0.045 1536 Dihedral : 5.669 55.507 1446 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.88 % Allowed : 19.09 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1123 helix: 2.04 (0.27), residues: 393 sheet: -0.05 (0.28), residues: 289 loop : -0.60 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 164 TYR 0.016 0.002 TYR H 50 PHE 0.021 0.002 PHE H 239 TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 9024) covalent geometry : angle 0.56304 / 0.29 (12265) SS BOND : bond 0.00027 / 0.01 ( 1) SS BOND : angle 0.86864 / 0.41 ( 2) hydrogen bonds : bond 0.03315 / 2.22 ( 433) hydrogen bonds : angle 4.14703 / 2.95 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.292 Fit side-chains REVERT: A 10 LYS cc_start: 0.8325 (mtmm) cc_final: 0.8071 (mtmm) REVERT: A 217 VAL cc_start: 0.8691 (p) cc_final: 0.8407 (m) REVERT: B 32 GLN cc_start: 0.7799 (mt0) cc_final: 0.7437 (mt0) REVERT: B 59 TYR cc_start: 0.8381 (m-80) cc_final: 0.8179 (m-80) REVERT: B 74 SER cc_start: 0.8732 (t) cc_final: 0.8204 (p) REVERT: B 134 ARG cc_start: 0.8279 (mtm110) cc_final: 0.7923 (mtm110) REVERT: B 243 THR cc_start: 0.7268 (p) cc_final: 0.7064 (p) REVERT: B 262 MET cc_start: 0.7303 (mmm) cc_final: 0.7083 (mmm) REVERT: C 21 LEU cc_start: 0.7751 (tp) cc_final: 0.7481 (tp) REVERT: C 53 THR cc_start: 0.7737 (t) cc_final: 0.7252 (p) REVERT: C 102 MET cc_start: 0.7538 (tpt) cc_final: 0.7036 (tpt) REVERT: G 32 LYS cc_start: 0.8557 (ttpp) cc_final: 0.8312 (ttpp) REVERT: H 32 PHE cc_start: 0.8592 (m-80) cc_final: 0.8167 (m-80) REVERT: H 103 TYR cc_start: 0.8538 (t80) cc_final: 0.7971 (t80) REVERT: H 155 VAL cc_start: 0.8230 (p) cc_final: 0.8023 (m) outliers start: 36 outliers final: 33 residues processed: 208 average time/residue: 0.0909 time to fit residues: 25.4190 Evaluate side-chains 223 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 246 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 55 optimal weight: 0.0010 chunk 91 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.137419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122716 restraints weight = 12207.319| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.90 r_work: 0.3464 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9025 Z= 0.147 Angle : 0.553 9.420 12267 Z= 0.286 Chirality : 0.041 0.150 1425 Planarity : 0.004 0.046 1536 Dihedral : 5.593 54.036 1446 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.78 % Allowed : 18.77 % Favored : 77.45 % 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 are not related in a simple way. whole: 0.72 (0.26), residues: 1123 helix: 2.06 (0.27), residues: 393 sheet: -0.06 (0.28), residues: 289 loop : -0.55 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 164 TYR 0.016 0.002 TYR H 50 PHE 0.020 0.002 PHE H 239 TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 9024) covalent geometry : angle 0.55327 / 0.29 (12265) SS BOND : bond 0.00078 / 0.04 ( 1) SS BOND : angle 0.84768 / 0.39 ( 2) hydrogen bonds : bond 0.03175 / 2.13 ( 433) hydrogen bonds : angle 4.12344 / 2.94 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.260 Fit side-chains REVERT: A 10 LYS cc_start: 0.8254 (mtmm) cc_final: 0.8022 (mtmm) REVERT: A 217 VAL cc_start: 0.8691 (p) cc_final: 0.8403 (m) REVERT: B 32 GLN cc_start: 0.7872 (mt0) cc_final: 0.7489 (mt0) REVERT: B 74 SER cc_start: 0.8702 (t) cc_final: 0.8148 (p) REVERT: B 86 THR cc_start: 0.8300 (p) cc_final: 0.7784 (t) REVERT: B 134 ARG cc_start: 0.8305 (mtm110) cc_final: 0.7943 (mtm110) REVERT: B 243 THR cc_start: 0.7211 (p) cc_final: 0.7004 (p) REVERT: B 262 MET cc_start: 0.7193 (mmm) cc_final: 0.6960 (mmm) REVERT: C 21 LEU cc_start: 0.7736 (tp) cc_final: 0.7466 (tp) REVERT: C 53 THR cc_start: 0.7707 (t) cc_final: 0.7225 (p) REVERT: C 102 MET cc_start: 0.7520 (tpt) cc_final: 0.7016 (tpt) REVERT: G 32 LYS cc_start: 0.8541 (ttpp) cc_final: 0.8316 (ttpp) REVERT: H 32 PHE cc_start: 0.8603 (m-80) cc_final: 0.8123 (m-80) REVERT: H 103 TYR cc_start: 0.8522 (t80) cc_final: 0.7936 (t80) REVERT: H 155 VAL cc_start: 0.8244 (p) cc_final: 0.8035 (m) outliers start: 35 outliers final: 33 residues processed: 206 average time/residue: 0.0801 time to fit residues: 22.2234 Evaluate side-chains 221 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 0.3980 chunk 109 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.121087 restraints weight = 12214.799| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.91 r_work: 0.3458 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9025 Z= 0.168 Angle : 0.571 9.551 12267 Z= 0.295 Chirality : 0.041 0.152 1425 Planarity : 0.004 0.046 1536 Dihedral : 5.603 52.891 1446 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.45 % Allowed : 19.53 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1123 helix: 2.03 (0.27), residues: 392 sheet: -0.07 (0.28), residues: 289 loop : -0.53 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 164 TYR 0.015 0.002 TYR H 190 PHE 0.027 0.002 PHE H 239 TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 9024) covalent geometry : angle 0.57097 / 0.30 (12265) SS BOND : bond 0.00168 / 0.09 ( 1) SS BOND : angle 0.73748 / 0.34 ( 2) hydrogen bonds : bond 0.03303 / 2.21 ( 433) hydrogen bonds : angle 4.18004 / 2.98 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.230 Fit side-chains REVERT: A 10 LYS cc_start: 0.8320 (mtmm) cc_final: 0.8081 (mtmm) REVERT: A 217 VAL cc_start: 0.8702 (p) cc_final: 0.8420 (m) REVERT: A 270 LEU cc_start: 0.8238 (mm) cc_final: 0.7933 (mp) REVERT: B 32 GLN cc_start: 0.7889 (mt0) cc_final: 0.7531 (mt0) REVERT: B 74 SER cc_start: 0.8733 (t) cc_final: 0.8298 (p) REVERT: B 86 THR cc_start: 0.8318 (p) cc_final: 0.7813 (t) REVERT: B 134 ARG cc_start: 0.8294 (mtm110) cc_final: 0.7937 (mtm110) REVERT: B 243 THR cc_start: 0.7206 (p) cc_final: 0.6991 (p) REVERT: B 259 GLN cc_start: 0.7668 (tt0) cc_final: 0.7466 (tt0) REVERT: C 21 LEU cc_start: 0.7760 (tp) cc_final: 0.7494 (tp) REVERT: C 53 THR cc_start: 0.7732 (t) cc_final: 0.7259 (p) REVERT: C 102 MET cc_start: 0.7517 (tpt) cc_final: 0.6986 (tpt) REVERT: G 32 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8315 (ttpp) REVERT: H 32 PHE cc_start: 0.8570 (m-80) cc_final: 0.8163 (m-80) REVERT: H 103 TYR cc_start: 0.8542 (t80) cc_final: 0.7965 (t80) REVERT: H 155 VAL cc_start: 0.8238 (p) cc_final: 0.8026 (m) outliers start: 32 outliers final: 31 residues processed: 209 average time/residue: 0.0884 time to fit residues: 24.8139 Evaluate side-chains 223 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 0.0070 chunk 23 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.121327 restraints weight = 12064.833| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.89 r_work: 0.3460 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9025 Z= 0.162 Angle : 0.575 9.631 12267 Z= 0.295 Chirality : 0.041 0.154 1425 Planarity : 0.004 0.046 1536 Dihedral : 5.581 52.104 1446 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.88 % Allowed : 19.42 % Favored : 76.70 % 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 are not related in a simple way. whole: 0.69 (0.26), residues: 1123 helix: 1.95 (0.27), residues: 395 sheet: -0.06 (0.28), residues: 289 loop : -0.50 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 164 TYR 0.015 0.002 TYR H 190 PHE 0.024 0.002 PHE H 29 TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 9024) covalent geometry : angle 0.57478 / 0.30 (12265) SS BOND : bond 0.00122 / 0.06 ( 1) SS BOND : angle 0.85408 / 0.39 ( 2) hydrogen bonds : bond 0.03263 / 2.18 ( 433) hydrogen bonds : angle 4.17327 / 2.97 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.52 seconds wall clock time: 34 minutes 46.19 seconds (2086.19 seconds total)