Starting phenix.real_space_refine on Sat Aug 23 01:27:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h8j_34549/08_2025/8h8j_34549_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h8j_34549/08_2025/8h8j_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 { model { file = "/net/cci-nas-00/data/ceres_data/8h8j_34549/08_2025/8h8j_34549_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h8j_34549/08_2025/8h8j_34549_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h8j_34549/08_2025/8h8j_34549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h8j_34549/08_2025/8h8j_34549.map" } 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-2.0-5787/lib/python3.9/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, 106 Unusual residues: {' CA': 1, 'CLR': 3, 'WYB': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 1.84, per 1000 atoms: 0.21 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: 0.69 Conformation dependent library (CDL) restraints added in 234.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.30 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: 1.47 Time building geometry restraints manager: 0.87 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: 1.100 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.450 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 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 aren 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 covalent geometry : bond 0.00341 ( 9024) covalent geometry : angle 0.66445 (12265) SS BOND : bond 0.00246 ( 1) SS BOND : angle 0.80765 ( 2) hydrogen bonds : bond 0.11809 ( 433) hydrogen bonds : angle 4.60156 ( 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 : 0.367 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: 0.7848 (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: 0.7513 (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: 0.6733 (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: 0.1054 time to fit residues: 37.9420 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 : 0.323 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3813 r_free = 0.3813 target = 0.140455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126221 restraints weight = 12454.035| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.90 r_work: 0.3537 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9025 Z= 0.149 Angle : 0.540 8.077 12267 Z= 0.279 Chirality : 0.040 0.136 1425 Planarity : 0.004 0.050 1536 Dihedral : 7.339 85.591 1461 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.13 % Allowed : 12.62 % 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 aren not related in a simple way. whole: 0.26 (0.26), residues: 1123 helix: 1.81 (0.27), residues: 393 sheet: -0.24 (0.28), residues: 280 loop : -1.00 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 167 TYR 0.017 0.002 TYR H 190 PHE 0.017 0.002 PHE A 212 TRP 0.016 0.002 TRP B 169 HIS 0.007 0.001 HIS H 167 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9024) covalent geometry : angle 0.54000 (12265) SS BOND : bond 0.00163 ( 1) SS BOND : angle 0.67366 ( 2) hydrogen bonds : bond 0.03069 ( 433) hydrogen bonds : angle 3.79838 ( 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 254 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.542 Fit side-chains REVERT: A 10 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7711 (mtmm) REVERT: B 25 CYS cc_start: 0.7857 (m) cc_final: 0.7533 (m) REVERT: B 32 GLN cc_start: 0.7534 (mt0) cc_final: 0.7098 (mt0) REVERT: B 134 ARG cc_start: 0.8188 (mtm110) cc_final: 0.7813 (mtm110) REVERT: B 249 THR cc_start: 0.7881 (p) cc_final: 0.7638 (t) REVERT: B 297 TRP cc_start: 0.8431 (m100) cc_final: 0.8147 (m100) REVERT: B 303 ASP cc_start: 0.7559 (p0) cc_final: 0.7190 (p0) REVERT: B 340 ASN cc_start: 0.7445 (m110) cc_final: 0.7090 (t0) REVERT: C 90 GLN cc_start: 0.8225 (mt0) cc_final: 0.7963 (mt0) REVERT: C 102 MET cc_start: 0.7433 (tpt) cc_final: 0.6969 (tpt) REVERT: C 123 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7647 (mtt-85) REVERT: G 21 MET cc_start: 0.8171 (tmm) cc_final: 0.7943 (tmm) REVERT: G 44 HIS cc_start: 0.8394 (m90) cc_final: 0.8168 (m90) outliers start: 29 outliers final: 14 residues processed: 239 average time/residue: 0.1073 time to fit residues: 35.0435 Evaluate side-chains 214 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 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: 0.0970 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS B 176 GLN B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.143933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128850 restraints weight = 12217.341| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.03 r_work: 0.3489 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9025 Z= 0.135 Angle : 0.517 7.309 12267 Z= 0.266 Chirality : 0.040 0.160 1425 Planarity : 0.004 0.051 1536 Dihedral : 5.913 58.076 1447 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.88 % Allowed : 14.67 % Favored : 81.45 % 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 aren not related in a simple way. whole: 0.56 (0.26), residues: 1123 helix: 2.05 (0.27), residues: 390 sheet: 0.05 (0.29), residues: 281 loop : -0.89 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 164 TYR 0.014 0.001 TYR H 190 PHE 0.025 0.002 PHE H 29 TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9024) covalent geometry : angle 0.51721 (12265) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.55784 ( 2) hydrogen bonds : bond 0.03024 ( 433) hydrogen bonds : angle 3.76801 ( 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 256 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.349 Fit side-chains REVERT: A 10 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7743 (mtmm) REVERT: A 51 ILE cc_start: 0.8741 (mm) cc_final: 0.8508 (mt) REVERT: A 217 VAL cc_start: 0.8568 (p) cc_final: 0.8229 (m) REVERT: B 32 GLN cc_start: 0.7588 (mt0) cc_final: 0.7301 (mt0) REVERT: B 59 TYR cc_start: 0.8386 (m-80) cc_final: 0.8133 (m-80) REVERT: B 75 GLN cc_start: 0.6877 (mt0) cc_final: 0.6606 (mt0) REVERT: B 134 ARG cc_start: 0.8236 (mtm110) cc_final: 0.7871 (mtm110) REVERT: B 249 THR cc_start: 0.7992 (p) cc_final: 0.7758 (t) REVERT: B 303 ASP cc_start: 0.7674 (p0) cc_final: 0.7297 (p0) REVERT: B 325 MET cc_start: 0.8086 (tpp) cc_final: 0.7731 (tpp) REVERT: C 21 LEU cc_start: 0.7644 (tp) cc_final: 0.7373 (tp) REVERT: C 90 GLN cc_start: 0.8286 (mt0) cc_final: 0.7994 (mt0) REVERT: C 102 MET cc_start: 0.7445 (tpt) cc_final: 0.6942 (tpt) REVERT: C 123 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7678 (mtt-85) REVERT: C 279 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6987 (mtm) REVERT: H 32 PHE cc_start: 0.8558 (m-80) cc_final: 0.8078 (m-80) outliers start: 36 outliers final: 23 residues processed: 238 average time/residue: 0.1039 time to fit residues: 33.6812 Evaluate side-chains 237 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 88 ASN 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 55 THR Chi-restraints excluded: chain C residue 112 VAL 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 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 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: 0.8980 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 82 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 340 ASN C 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121599 restraints weight = 12452.088| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.03 r_work: 0.3459 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2559 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= 0.160 Angle : 0.536 7.798 12267 Z= 0.277 Chirality : 0.041 0.139 1425 Planarity : 0.004 0.049 1536 Dihedral : 5.718 57.754 1447 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.21 % Allowed : 16.40 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.26), residues: 1123 helix: 2.15 (0.27), residues: 387 sheet: 0.10 (0.29), residues: 281 loop : -0.78 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 164 TYR 0.019 0.002 TYR H 190 PHE 0.018 0.002 PHE H 29 TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9024) covalent geometry : angle 0.53624 (12265) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.65044 ( 2) hydrogen bonds : bond 0.03135 ( 433) hydrogen bonds : angle 3.90095 ( 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: 39 poor density : 219 time to evaluate : 0.331 Fit side-chains REVERT: B 32 GLN cc_start: 0.7662 (mt0) cc_final: 0.7305 (mt0) REVERT: B 59 TYR cc_start: 0.8395 (m-80) cc_final: 0.8167 (m-80) REVERT: B 74 SER cc_start: 0.8585 (t) cc_final: 0.8338 (t) REVERT: B 75 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6785 (mt0) REVERT: B 134 ARG cc_start: 0.8327 (mtm110) cc_final: 0.7924 (mtm110) REVERT: B 249 THR cc_start: 0.8136 (p) cc_final: 0.7878 (t) REVERT: B 262 MET cc_start: 0.7266 (mmm) cc_final: 0.7063 (mmm) REVERT: B 303 ASP cc_start: 0.7717 (p0) cc_final: 0.7316 (p0) REVERT: B 325 MET cc_start: 0.8118 (tpp) cc_final: 0.7871 (tpp) REVERT: C 21 LEU cc_start: 0.7727 (tp) cc_final: 0.7454 (tp) REVERT: C 53 THR cc_start: 0.7620 (t) cc_final: 0.7080 (p) REVERT: C 64 VAL cc_start: 0.7986 (t) cc_final: 0.7721 (p) REVERT: C 90 GLN cc_start: 0.8320 (mt0) cc_final: 0.8014 (mt0) REVERT: C 102 MET cc_start: 0.7434 (tpt) cc_final: 0.6937 (tpt) REVERT: C 123 ARG cc_start: 0.7960 (mtt-85) cc_final: 0.7759 (mtt-85) REVERT: C 163 PHE cc_start: 0.8026 (m-10) cc_final: 0.7687 (m-10) REVERT: C 279 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7024 (mtm) REVERT: H 155 VAL cc_start: 0.8256 (p) cc_final: 0.7989 (m) outliers start: 39 outliers final: 28 residues processed: 239 average time/residue: 0.0979 time to fit residues: 32.1187 Evaluate side-chains 245 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 82 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 55 THR Chi-restraints excluded: chain C residue 148 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 250 LEU Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 279 MET 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 187 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.9990 chunk 85 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN 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 = 0.3761 r_free = 0.3761 target = 0.136821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.121980 restraints weight = 12365.098| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.93 r_work: 0.3470 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9025 Z= 0.140 Angle : 0.530 8.230 12267 Z= 0.274 Chirality : 0.040 0.147 1425 Planarity : 0.004 0.047 1536 Dihedral : 5.665 59.875 1447 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.56 % Allowed : 18.55 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.26), residues: 1123 helix: 2.20 (0.27), residues: 387 sheet: 0.10 (0.29), residues: 281 loop : -0.74 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.016 0.002 TYR B 289 PHE 0.016 0.001 PHE H 29 TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9024) covalent geometry : angle 0.53019 (12265) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.63762 ( 2) hydrogen bonds : bond 0.03060 ( 433) hydrogen bonds : angle 3.89958 ( 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 245 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.343 Fit side-chains REVERT: A 213 GLU cc_start: 0.6557 (mp0) cc_final: 0.6269 (mp0) REVERT: A 217 VAL cc_start: 0.8674 (p) cc_final: 0.8327 (m) REVERT: B 32 GLN cc_start: 0.7793 (mt0) cc_final: 0.7426 (mt0) REVERT: B 59 TYR cc_start: 0.8397 (m-80) cc_final: 0.8176 (m-80) REVERT: B 74 SER cc_start: 0.8610 (t) cc_final: 0.8355 (t) REVERT: B 75 GLN cc_start: 0.7017 (mt0) cc_final: 0.6788 (mt0) REVERT: B 134 ARG cc_start: 0.8333 (mtm110) cc_final: 0.7945 (mtm110) REVERT: B 165 THR cc_start: 0.7829 (p) cc_final: 0.7618 (p) REVERT: B 249 THR cc_start: 0.8080 (p) cc_final: 0.7833 (t) REVERT: B 303 ASP cc_start: 0.7699 (p0) cc_final: 0.7294 (p0) REVERT: C 21 LEU cc_start: 0.7683 (tp) cc_final: 0.7413 (tp) REVERT: C 90 GLN cc_start: 0.8303 (mt0) cc_final: 0.7993 (mt0) REVERT: C 102 MET cc_start: 0.7526 (tpt) cc_final: 0.7017 (tpt) REVERT: C 163 PHE cc_start: 0.8043 (m-10) cc_final: 0.7737 (m-10) REVERT: C 279 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.7005 (mtm) REVERT: H 32 PHE cc_start: 0.8591 (m-80) cc_final: 0.8091 (m-80) REVERT: H 155 VAL cc_start: 0.8253 (p) cc_final: 0.8010 (m) outliers start: 33 outliers final: 28 residues processed: 230 average time/residue: 0.1032 time to fit residues: 32.0435 Evaluate side-chains 236 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 82 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 178 LEU 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 279 MET 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 172 THR Chi-restraints excluded: chain H residue 186 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 54 optimal weight: 0.0040 chunk 90 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 95 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 220 GLN B 230 ASN B 340 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 = 0.3764 r_free = 0.3764 target = 0.136950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.121857 restraints weight = 12354.883| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.01 r_work: 0.3466 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9025 Z= 0.131 Angle : 0.528 8.458 12267 Z= 0.272 Chirality : 0.040 0.140 1425 Planarity : 0.004 0.046 1536 Dihedral : 5.585 58.414 1447 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.31 % Allowed : 18.34 % 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 aren not related in a simple way. whole: 0.78 (0.26), residues: 1123 helix: 2.17 (0.27), residues: 390 sheet: 0.15 (0.29), residues: 280 loop : -0.70 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 123 TYR 0.016 0.001 TYR H 190 PHE 0.013 0.001 PHE H 29 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9024) covalent geometry : angle 0.52789 (12265) SS BOND : bond 0.00080 ( 1) SS BOND : angle 0.63698 ( 2) hydrogen bonds : bond 0.03017 ( 433) hydrogen bonds : angle 3.90263 ( 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 254 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 0.288 Fit side-chains REVERT: A 213 GLU cc_start: 0.6647 (mp0) cc_final: 0.6342 (mp0) REVERT: A 217 VAL cc_start: 0.8672 (p) cc_final: 0.8310 (m) REVERT: B 32 GLN cc_start: 0.7791 (mt0) cc_final: 0.7421 (mt0) REVERT: B 55 LEU cc_start: 0.8059 (mp) cc_final: 0.7843 (mt) REVERT: B 74 SER cc_start: 0.8613 (t) cc_final: 0.8037 (p) REVERT: B 75 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6839 (mt0) REVERT: B 134 ARG cc_start: 0.8314 (mtm110) cc_final: 0.7916 (mtm110) REVERT: B 249 THR cc_start: 0.8042 (p) cc_final: 0.7800 (t) REVERT: B 262 MET cc_start: 0.7317 (mmm) cc_final: 0.7033 (mmm) REVERT: B 303 ASP cc_start: 0.7720 (p0) cc_final: 0.7294 (p0) REVERT: C 21 LEU cc_start: 0.7708 (tp) cc_final: 0.7433 (tp) REVERT: C 53 THR cc_start: 0.7615 (t) cc_final: 0.7061 (p) REVERT: C 90 GLN cc_start: 0.8314 (mt0) cc_final: 0.7974 (mt0) REVERT: C 102 MET cc_start: 0.7505 (tpt) cc_final: 0.6978 (tpt) REVERT: C 163 PHE cc_start: 0.8046 (m-10) cc_final: 0.7727 (m-10) REVERT: C 279 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6993 (mtm) REVERT: H 32 PHE cc_start: 0.8544 (m-80) cc_final: 0.8133 (m-80) REVERT: H 155 VAL cc_start: 0.8253 (p) cc_final: 0.8001 (m) REVERT: H 177 PHE cc_start: 0.8270 (m-10) cc_final: 0.8038 (m-10) outliers start: 40 outliers final: 31 residues processed: 233 average time/residue: 0.0995 time to fit residues: 31.2337 Evaluate side-chains 245 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 250 CYS 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 279 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 0.0570 chunk 82 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 176 GLN B 220 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121153 restraints weight = 12408.582| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.04 r_work: 0.3449 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9025 Z= 0.136 Angle : 0.534 8.468 12267 Z= 0.274 Chirality : 0.040 0.141 1425 Planarity : 0.004 0.045 1536 Dihedral : 5.524 57.130 1446 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.31 % Allowed : 18.55 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.26), residues: 1123 helix: 2.15 (0.27), residues: 393 sheet: 0.18 (0.29), residues: 279 loop : -0.65 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 164 TYR 0.016 0.001 TYR H 190 PHE 0.023 0.001 PHE H 29 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9024) covalent geometry : angle 0.53376 (12265) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.63724 ( 2) hydrogen bonds : bond 0.03044 ( 433) hydrogen bonds : angle 3.93385 ( 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 253 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8219 (mt) cc_final: 0.8014 (mp) REVERT: A 217 VAL cc_start: 0.8615 (p) cc_final: 0.8318 (m) REVERT: B 32 GLN cc_start: 0.7822 (mt0) cc_final: 0.7449 (mt0) REVERT: B 59 TYR cc_start: 0.8416 (m-80) cc_final: 0.8152 (m-80) REVERT: B 74 SER cc_start: 0.8641 (t) cc_final: 0.8048 (p) REVERT: B 134 ARG cc_start: 0.8322 (mtm110) cc_final: 0.7929 (mtm110) REVERT: B 262 MET cc_start: 0.7328 (mmm) cc_final: 0.7070 (mmm) REVERT: C 21 LEU cc_start: 0.7757 (tp) cc_final: 0.7483 (tp) REVERT: C 53 THR cc_start: 0.7654 (t) cc_final: 0.7112 (p) REVERT: C 90 GLN cc_start: 0.8334 (mt0) cc_final: 0.7987 (mt0) REVERT: C 102 MET cc_start: 0.7528 (tpt) cc_final: 0.7019 (tpt) REVERT: C 163 PHE cc_start: 0.8074 (m-10) cc_final: 0.7742 (m-10) REVERT: C 279 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7044 (mtm) REVERT: H 32 PHE cc_start: 0.8584 (m-80) cc_final: 0.8132 (m-80) REVERT: H 155 VAL cc_start: 0.8260 (p) cc_final: 0.8017 (m) outliers start: 40 outliers final: 32 residues processed: 234 average time/residue: 0.1006 time to fit residues: 32.0486 Evaluate side-chains 237 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 250 CYS 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 67 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 279 MET 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 172 THR Chi-restraints excluded: chain H residue 186 GLN 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: 0.0470 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 104 optimal weight: 0.0870 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121545 restraints weight = 12337.993| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.91 r_work: 0.3460 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9025 Z= 0.138 Angle : 0.548 8.179 12267 Z= 0.280 Chirality : 0.041 0.146 1425 Planarity : 0.004 0.045 1536 Dihedral : 5.498 56.065 1446 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.21 % Allowed : 18.88 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1123 helix: 2.19 (0.27), residues: 393 sheet: 0.16 (0.29), residues: 279 loop : -0.60 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 164 TYR 0.016 0.001 TYR H 190 PHE 0.020 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 covalent geometry : bond 0.00310 ( 9024) covalent geometry : angle 0.54820 (12265) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.64303 ( 2) hydrogen bonds : bond 0.03061 ( 433) hydrogen bonds : angle 3.95487 ( 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 244 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 217 VAL cc_start: 0.8616 (p) cc_final: 0.8316 (m) REVERT: B 32 GLN cc_start: 0.7800 (mt0) cc_final: 0.7417 (mt0) REVERT: B 59 TYR cc_start: 0.8400 (m-80) cc_final: 0.7763 (m-80) REVERT: B 74 SER cc_start: 0.8704 (t) cc_final: 0.7983 (p) REVERT: B 75 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.6309 (mt0) REVERT: B 134 ARG cc_start: 0.8297 (mtm110) cc_final: 0.7911 (mtm110) REVERT: B 262 MET cc_start: 0.7268 (mmm) cc_final: 0.7030 (mmm) REVERT: B 303 ASP cc_start: 0.7764 (p0) cc_final: 0.7416 (p0) REVERT: C 21 LEU cc_start: 0.7750 (tp) cc_final: 0.7479 (tp) REVERT: C 53 THR cc_start: 0.7638 (t) cc_final: 0.7113 (p) REVERT: C 90 GLN cc_start: 0.8312 (mt0) cc_final: 0.7949 (mt0) REVERT: C 102 MET cc_start: 0.7481 (tpt) cc_final: 0.6971 (tpt) REVERT: C 163 PHE cc_start: 0.8056 (m-10) cc_final: 0.7726 (m-10) REVERT: H 32 PHE cc_start: 0.8609 (m-80) cc_final: 0.8128 (m-80) REVERT: H 155 VAL cc_start: 0.8250 (p) cc_final: 0.8013 (m) outliers start: 39 outliers final: 30 residues processed: 225 average time/residue: 0.0980 time to fit residues: 29.7087 Evaluate side-chains 233 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 43 ILE Chi-restraints excluded: chain B residue 75 GLN 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 250 CYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 35 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 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 172 THR Chi-restraints excluded: chain H residue 186 GLN 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: 0.5980 chunk 107 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 100 optimal weight: 0.0170 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 29 optimal weight: 0.5980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.136580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121939 restraints weight = 12213.092| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.89 r_work: 0.3466 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9025 Z= 0.129 Angle : 0.546 9.062 12267 Z= 0.279 Chirality : 0.040 0.145 1425 Planarity : 0.004 0.045 1536 Dihedral : 5.432 54.642 1446 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.56 % Allowed : 19.63 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.26), residues: 1123 helix: 2.17 (0.27), residues: 394 sheet: 0.23 (0.30), residues: 279 loop : -0.53 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 164 TYR 0.017 0.001 TYR H 190 PHE 0.022 0.002 PHE H 29 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9024) covalent geometry : angle 0.54594 (12265) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.67592 ( 2) hydrogen bonds : bond 0.03009 ( 433) hydrogen bonds : angle 3.96048 ( 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 237 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.335 Fit side-chains REVERT: A 217 VAL cc_start: 0.8607 (p) cc_final: 0.8305 (m) REVERT: B 32 GLN cc_start: 0.7778 (mt0) cc_final: 0.7480 (mt0) REVERT: B 59 TYR cc_start: 0.8393 (m-80) cc_final: 0.8092 (m-80) REVERT: B 74 SER cc_start: 0.8737 (t) cc_final: 0.7991 (p) REVERT: B 75 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6400 (mt0) REVERT: B 134 ARG cc_start: 0.8289 (mtm110) cc_final: 0.7905 (mtm110) REVERT: B 262 MET cc_start: 0.7181 (mmm) cc_final: 0.6959 (mmm) REVERT: B 303 ASP cc_start: 0.7809 (p0) cc_final: 0.7442 (p0) REVERT: C 21 LEU cc_start: 0.7736 (tp) cc_final: 0.7461 (tp) REVERT: C 53 THR cc_start: 0.7644 (t) cc_final: 0.7103 (p) REVERT: C 90 GLN cc_start: 0.8328 (mt0) cc_final: 0.7958 (mt0) REVERT: C 102 MET cc_start: 0.7469 (tpt) cc_final: 0.6957 (tpt) REVERT: H 32 PHE cc_start: 0.8575 (m-80) cc_final: 0.8119 (m-80) REVERT: H 155 VAL cc_start: 0.8249 (p) cc_final: 0.8011 (m) outliers start: 33 outliers final: 27 residues processed: 219 average time/residue: 0.0974 time to fit residues: 28.6966 Evaluate side-chains 230 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 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 75 GLN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 67 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 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 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122006 restraints weight = 12203.242| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.91 r_work: 0.3474 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9025 Z= 0.169 Angle : 0.583 10.174 12267 Z= 0.298 Chirality : 0.042 0.155 1425 Planarity : 0.004 0.046 1536 Dihedral : 5.553 53.719 1446 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.24 % Allowed : 20.06 % 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 aren not related in a simple way. whole: 0.85 (0.26), residues: 1123 helix: 2.15 (0.27), residues: 393 sheet: 0.14 (0.30), residues: 278 loop : -0.55 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 164 TYR 0.016 0.002 TYR H 190 PHE 0.043 0.002 PHE C 163 TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9024) covalent geometry : angle 0.58274 (12265) SS BOND : bond 0.00057 ( 1) SS BOND : angle 1.10481 ( 2) hydrogen bonds : bond 0.03212 ( 433) hydrogen bonds : angle 4.07829 ( 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 229 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 217 VAL cc_start: 0.8666 (p) cc_final: 0.8371 (m) REVERT: A 270 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7938 (mp) REVERT: B 32 GLN cc_start: 0.7858 (mt0) cc_final: 0.7493 (mt0) REVERT: B 59 TYR cc_start: 0.8410 (m-80) cc_final: 0.8148 (m-80) REVERT: B 74 SER cc_start: 0.8742 (t) cc_final: 0.8103 (p) REVERT: B 134 ARG cc_start: 0.8308 (mtm110) cc_final: 0.7940 (mtm110) REVERT: B 258 ASP cc_start: 0.7654 (t0) cc_final: 0.7447 (t70) REVERT: B 262 MET cc_start: 0.7237 (mmm) cc_final: 0.7002 (mmm) REVERT: B 303 ASP cc_start: 0.7839 (p0) cc_final: 0.7507 (p0) REVERT: C 21 LEU cc_start: 0.7734 (tp) cc_final: 0.7463 (tp) REVERT: C 53 THR cc_start: 0.7709 (t) cc_final: 0.7219 (p) REVERT: C 102 MET cc_start: 0.7540 (tpt) cc_final: 0.7037 (tpt) REVERT: C 113 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7557 (t0) REVERT: H 32 PHE cc_start: 0.8616 (m-80) cc_final: 0.8172 (m-80) REVERT: H 103 TYR cc_start: 0.8494 (t80) cc_final: 0.8082 (t80) REVERT: H 155 VAL cc_start: 0.8246 (p) cc_final: 0.8040 (m) outliers start: 30 outliers final: 27 residues processed: 212 average time/residue: 0.1112 time to fit residues: 31.6433 Evaluate side-chains 221 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 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 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 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 113 ASP 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 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 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: 0.9980 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 106 optimal weight: 0.0020 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.137928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123312 restraints weight = 12105.168| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.91 r_work: 0.3491 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3240 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= 0.128 Angle : 0.556 8.601 12267 Z= 0.286 Chirality : 0.040 0.146 1425 Planarity : 0.004 0.046 1536 Dihedral : 5.441 52.608 1446 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.45 % Allowed : 19.85 % 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 aren not related in a simple way. whole: 0.91 (0.26), residues: 1123 helix: 2.21 (0.27), residues: 393 sheet: 0.16 (0.30), residues: 278 loop : -0.51 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 164 TYR 0.018 0.001 TYR H 190 PHE 0.036 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 covalent geometry : bond 0.00289 ( 9024) covalent geometry : angle 0.55600 (12265) SS BOND : bond 0.00204 ( 1) SS BOND : angle 1.01580 ( 2) hydrogen bonds : bond 0.03055 ( 433) hydrogen bonds : angle 4.04625 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2499.52 seconds wall clock time: 43 minutes 39.47 seconds (2619.47 seconds total)