Starting phenix.real_space_refine on Fri Aug 22 22:02:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzs_27807/08_2025/8dzs_27807.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzs_27807/08_2025/8dzs_27807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dzs_27807/08_2025/8dzs_27807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzs_27807/08_2025/8dzs_27807.map" model { file = "/net/cci-nas-00/data/ceres_data/8dzs_27807/08_2025/8dzs_27807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzs_27807/08_2025/8dzs_27807.cif" } resolution = 2.65 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 53 5.16 5 Cl 2 4.86 5 C 5283 2.51 5 N 1381 2.21 5 O 1526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 8245 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2047 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 261} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 5, 'TYR:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1641 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 209} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2482 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 5, 'ARG:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 336 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1712 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'U9I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.23, per 1000 atoms: 0.27 Number of scatterers: 8245 At special positions: 0 Unit cell: (90.64, 118.8, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 53 16.00 O 1526 8.00 N 1381 7.00 C 5283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 0.55 Conformation dependent library (CDL) restraints added in 618.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 36.5% alpha, 24.8% 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 60 through 63 Processing helix chain 'A' and resid 64 through 87 removed outlier: 3.541A pdb=" N VAL A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A 70 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 110 removed outlier: 3.708A pdb=" N ILE A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 4.282A pdb=" N VAL A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 162 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 171 through 196 removed outlier: 3.678A pdb=" N SER A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.839A pdb=" N ASP A 223 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 264 through 300 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 307 through 332 removed outlier: 3.756A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.596A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.531A pdb=" N LYS B 211 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 217 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 256 removed outlier: 3.617A pdb=" N ASN B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 279 removed outlier: 4.053A pdb=" N ALA B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 311 removed outlier: 3.783A pdb=" N LEU B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 352 removed outlier: 3.986A pdb=" N LYS B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 4.070A pdb=" N ARG C 8 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.511A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 removed outlier: 4.258A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 12 through 22 removed outlier: 3.655A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.946A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.622A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 199 through 201 Processing sheet with id=AA2, first strand: chain 'B' and resid 186 through 191 removed outlier: 6.460A pdb=" N ILE B 34 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL B 200 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU B 36 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N ALA B 221 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.073A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.537A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 4.459A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 4.237A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.849A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.652A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.589A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.451A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.451A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.653A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 148 418 hydrogen bonds defined for protein. 1185 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: 1.35 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2405 1.34 - 1.46: 2223 1.46 - 1.59: 3702 1.59 - 1.71: 0 1.71 - 1.84: 76 Bond restraints: 8406 Sorted by residual: bond pdb=" C16 U9I A 501 " pdb=" C17 U9I A 501 " ideal model delta sigma weight residual 1.548 1.512 0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C17 U9I A 501 " pdb=" C18 U9I A 501 " ideal model delta sigma weight residual 1.541 1.505 0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C3 U9I A 501 " pdb=" C4 U9I A 501 " ideal model delta sigma weight residual 1.527 1.496 0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" CA THR E 198 " pdb=" C THR E 198 " ideal model delta sigma weight residual 1.526 1.553 -0.027 1.75e-02 3.27e+03 2.37e+00 bond pdb=" CB CYS E 96 " pdb=" SG CYS E 96 " ideal model delta sigma weight residual 1.808 1.759 0.049 3.30e-02 9.18e+02 2.17e+00 ... (remaining 8401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 11157 2.11 - 4.22: 231 4.22 - 6.32: 25 6.32 - 8.43: 12 8.43 - 10.54: 4 Bond angle restraints: 11429 Sorted by residual: angle pdb=" CA THR E 198 " pdb=" CB THR E 198 " pdb=" CG2 THR E 198 " ideal model delta sigma weight residual 110.50 116.12 -5.62 1.70e+00 3.46e-01 1.09e+01 angle pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C ARG B 313 " pdb=" N ASN B 314 " pdb=" CA ASN B 314 " ideal model delta sigma weight residual 122.82 126.98 -4.16 1.42e+00 4.96e-01 8.59e+00 angle pdb=" CA CYS A 210 " pdb=" CB CYS A 210 " pdb=" SG CYS A 210 " ideal model delta sigma weight residual 114.40 120.85 -6.45 2.30e+00 1.89e-01 7.86e+00 angle pdb=" CA ASP C 153 " pdb=" C ASP C 153 " pdb=" O ASP C 153 " ideal model delta sigma weight residual 121.14 118.29 2.85 1.03e+00 9.43e-01 7.64e+00 ... (remaining 11424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.02: 4684 23.02 - 46.04: 233 46.04 - 69.07: 23 69.07 - 92.09: 14 92.09 - 115.11: 2 Dihedral angle restraints: 4956 sinusoidal: 1767 harmonic: 3189 Sorted by residual: dihedral pdb=" CA GLN B 240 " pdb=" C GLN B 240 " pdb=" N THR B 241 " pdb=" CA THR B 241 " ideal model delta harmonic sigma weight residual -180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA THR E 160 " pdb=" C THR E 160 " pdb=" N TYR E 161 " pdb=" CA TYR E 161 " ideal model delta harmonic sigma weight residual -180.00 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 4953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 907 0.044 - 0.089: 329 0.089 - 0.133: 107 0.133 - 0.177: 11 0.177 - 0.222: 2 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CG LEU C 284 " pdb=" CB LEU C 284 " pdb=" CD1 LEU C 284 " pdb=" CD2 LEU C 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU E 162 " pdb=" CB LEU E 162 " pdb=" CD1 LEU E 162 " pdb=" CD2 LEU E 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE A 242 " pdb=" CA ILE A 242 " pdb=" CG1 ILE A 242 " pdb=" CG2 ILE A 242 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.66e-01 ... (remaining 1353 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 U9I A 501 " -0.039 2.00e-02 2.50e+03 3.99e-02 2.38e+01 pdb=" C4 U9I A 501 " 0.053 2.00e-02 2.50e+03 pdb=" C5 U9I A 501 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U9I A 501 " -0.043 2.00e-02 2.50e+03 pdb=" N2 U9I A 501 " -0.021 2.00e-02 2.50e+03 pdb=" O3 U9I A 501 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 198 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C THR E 198 " -0.056 2.00e-02 2.50e+03 pdb=" O THR E 198 " 0.021 2.00e-02 2.50e+03 pdb=" N ALA E 199 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 337 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C PHE B 337 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE B 337 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP B 338 " 0.012 2.00e-02 2.50e+03 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1810 2.78 - 3.31: 7394 3.31 - 3.84: 13653 3.84 - 4.37: 16284 4.37 - 4.90: 28218 Nonbonded interactions: 67359 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD2 ASP C 333 " model vdw 2.253 3.040 nonbonded pdb=" O VAL A 60 " pdb=" OG1 THR A 63 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR A 66 " pdb=" O TYR A 313 " model vdw 2.283 3.040 nonbonded pdb=" O THR A 150 " pdb=" OG SER A 153 " model vdw 2.291 3.040 nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.305 3.040 ... (remaining 67354 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 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 : 0.004 0.049 8408 Z= 0.193 Angle : 0.761 10.541 11433 Z= 0.398 Chirality : 0.050 0.222 1356 Planarity : 0.005 0.050 1425 Dihedral : 14.480 115.111 2888 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.12 % Allowed : 0.47 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.24), residues: 1074 helix: -0.31 (0.26), residues: 348 sheet: -0.18 (0.29), residues: 294 loop : -1.17 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.014 0.002 TYR E 178 PHE 0.030 0.002 PHE A 169 TRP 0.014 0.002 TRP C 63 HIS 0.007 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8406) covalent geometry : angle 0.75884 (11429) SS BOND : bond 0.00304 ( 2) SS BOND : angle 2.82362 ( 4) hydrogen bonds : bond 0.15159 ( 414) hydrogen bonds : angle 7.06553 ( 1185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.280 Fit side-chains REVERT: C 188 MET cc_start: 0.8086 (mmp) cc_final: 0.7526 (mmm) REVERT: E 219 GLN cc_start: 0.8650 (pp30) cc_final: 0.8443 (pp30) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.4236 time to fit residues: 80.4470 Evaluate side-chains 172 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 254 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 312 ASN C 220 GLN C 268 ASN E 77 ASN E 82 GLN E 174 GLN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.141845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127306 restraints weight = 11765.410| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.66 r_work: 0.3623 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8408 Z= 0.180 Angle : 0.600 7.527 11433 Z= 0.316 Chirality : 0.044 0.154 1356 Planarity : 0.004 0.042 1425 Dihedral : 7.875 113.619 1203 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.13 % Allowed : 10.63 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.61 (0.25), residues: 1074 helix: 0.34 (0.26), residues: 364 sheet: -0.22 (0.30), residues: 292 loop : -1.08 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 15 TYR 0.015 0.002 TYR E 178 PHE 0.016 0.002 PHE A 70 TRP 0.013 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8406) covalent geometry : angle 0.59819 (11429) SS BOND : bond 0.00338 ( 2) SS BOND : angle 2.45678 ( 4) hydrogen bonds : bond 0.05166 ( 414) hydrogen bonds : angle 5.23406 ( 1185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.316 Fit side-chains REVERT: A 178 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7418 (mm) REVERT: C 290 ASP cc_start: 0.7003 (m-30) cc_final: 0.6799 (m-30) REVERT: E 219 GLN cc_start: 0.8738 (pp30) cc_final: 0.8467 (pp30) outliers start: 18 outliers final: 4 residues processed: 174 average time/residue: 0.4698 time to fit residues: 87.9684 Evaluate side-chains 176 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 171 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 133 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 16 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 257 ASN B 312 ASN B 314 ASN C 266 HIS E 77 ASN E 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.141715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.127385 restraints weight = 11659.159| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.64 r_work: 0.3621 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8408 Z= 0.170 Angle : 0.570 7.995 11433 Z= 0.301 Chirality : 0.044 0.147 1356 Planarity : 0.003 0.039 1425 Dihedral : 7.219 106.442 1201 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.95 % Allowed : 11.92 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.39 (0.25), residues: 1074 helix: 0.71 (0.27), residues: 361 sheet: -0.17 (0.30), residues: 287 loop : -1.08 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 15 TYR 0.015 0.002 TYR E 178 PHE 0.015 0.001 PHE A 70 TRP 0.012 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8406) covalent geometry : angle 0.56822 (11429) SS BOND : bond 0.00364 ( 2) SS BOND : angle 2.23005 ( 4) hydrogen bonds : bond 0.04854 ( 414) hydrogen bonds : angle 5.10302 ( 1185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: C 153 ASP cc_start: 0.7871 (p0) cc_final: 0.7647 (p0) REVERT: E 19 LYS cc_start: 0.8338 (tptm) cc_final: 0.8132 (tppt) outliers start: 25 outliers final: 15 residues processed: 181 average time/residue: 0.5103 time to fit residues: 98.8982 Evaluate side-chains 183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 ASN B 257 ASN C 220 GLN C 237 ASN C 239 ASN C 268 ASN C 340 ASN E 77 ASN E 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.139163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.124689 restraints weight = 11821.742| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.65 r_work: 0.3584 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8408 Z= 0.264 Angle : 0.640 8.104 11433 Z= 0.338 Chirality : 0.047 0.161 1356 Planarity : 0.004 0.043 1425 Dihedral : 7.394 104.747 1201 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.60 % Allowed : 14.99 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.55 (0.25), residues: 1074 helix: 0.47 (0.27), residues: 365 sheet: -0.27 (0.29), residues: 292 loop : -1.06 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 148 TYR 0.016 0.002 TYR A 313 PHE 0.020 0.002 PHE A 70 TRP 0.014 0.002 TRP C 63 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 8406) covalent geometry : angle 0.63788 (11429) SS BOND : bond 0.00367 ( 2) SS BOND : angle 2.79924 ( 4) hydrogen bonds : bond 0.05414 ( 414) hydrogen bonds : angle 5.24209 ( 1185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.325 Fit side-chains REVERT: A 65 VAL cc_start: 0.7731 (p) cc_final: 0.7518 (t) REVERT: C 153 ASP cc_start: 0.7879 (p0) cc_final: 0.7662 (p0) REVERT: C 304 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7307 (mtp-110) REVERT: E 19 LYS cc_start: 0.8436 (tptm) cc_final: 0.8198 (tppt) outliers start: 22 outliers final: 17 residues processed: 179 average time/residue: 0.4123 time to fit residues: 79.7370 Evaluate side-chains 191 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 257 ASN B 312 ASN C 237 ASN C 239 ASN E 77 ASN E 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.140758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.126536 restraints weight = 11726.935| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.63 r_work: 0.3611 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8408 Z= 0.160 Angle : 0.566 8.613 11433 Z= 0.298 Chirality : 0.043 0.144 1356 Planarity : 0.003 0.040 1425 Dihedral : 6.977 97.976 1201 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.83 % Allowed : 16.29 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.35 (0.26), residues: 1074 helix: 0.75 (0.27), residues: 367 sheet: -0.26 (0.29), residues: 294 loop : -1.00 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.015 0.001 TYR E 178 PHE 0.014 0.001 PHE A 70 TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8406) covalent geometry : angle 0.56498 (11429) SS BOND : bond 0.00394 ( 2) SS BOND : angle 2.16943 ( 4) hydrogen bonds : bond 0.04704 ( 414) hydrogen bonds : angle 5.04745 ( 1185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 65 VAL cc_start: 0.7748 (p) cc_final: 0.7533 (t) outliers start: 24 outliers final: 16 residues processed: 182 average time/residue: 0.4061 time to fit residues: 79.5121 Evaluate side-chains 188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 47 optimal weight: 0.3980 chunk 3 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN B 257 ASN C 268 ASN C 340 ASN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.142147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127912 restraints weight = 11728.339| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.64 r_work: 0.3630 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8408 Z= 0.123 Angle : 0.533 12.679 11433 Z= 0.280 Chirality : 0.042 0.134 1356 Planarity : 0.003 0.037 1425 Dihedral : 6.586 86.905 1201 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.36 % Allowed : 17.83 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.09 (0.26), residues: 1074 helix: 1.13 (0.28), residues: 362 sheet: -0.14 (0.30), residues: 289 loop : -0.97 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 148 TYR 0.015 0.001 TYR E 178 PHE 0.013 0.001 PHE A 70 TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8406) covalent geometry : angle 0.53218 (11429) SS BOND : bond 0.00343 ( 2) SS BOND : angle 1.87000 ( 4) hydrogen bonds : bond 0.04176 ( 414) hydrogen bonds : angle 4.87337 ( 1185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.207 Fit side-chains REVERT: A 151 MET cc_start: 0.7959 (mmm) cc_final: 0.7731 (tmm) outliers start: 20 outliers final: 15 residues processed: 171 average time/residue: 0.4138 time to fit residues: 76.1003 Evaluate side-chains 183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 74 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 ASN C 268 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.129500 restraints weight = 11726.985| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.64 r_work: 0.3614 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8408 Z= 0.162 Angle : 0.564 10.322 11433 Z= 0.295 Chirality : 0.043 0.146 1356 Planarity : 0.003 0.038 1425 Dihedral : 6.548 82.406 1201 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.72 % Allowed : 18.18 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.15 (0.26), residues: 1074 helix: 1.02 (0.27), residues: 367 sheet: -0.15 (0.30), residues: 289 loop : -0.99 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 148 TYR 0.014 0.001 TYR E 178 PHE 0.025 0.002 PHE A 169 TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8406) covalent geometry : angle 0.56263 (11429) SS BOND : bond 0.00395 ( 2) SS BOND : angle 2.07016 ( 4) hydrogen bonds : bond 0.04497 ( 414) hydrogen bonds : angle 4.95241 ( 1185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.364 Fit side-chains REVERT: A 151 MET cc_start: 0.7959 (mmm) cc_final: 0.7722 (tmm) REVERT: B 198 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8138 (ttpm) REVERT: C 49 ARG cc_start: 0.8633 (mpt180) cc_final: 0.8425 (mpt180) outliers start: 23 outliers final: 19 residues processed: 177 average time/residue: 0.4207 time to fit residues: 80.2185 Evaluate side-chains 189 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 103 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.142424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.128274 restraints weight = 11709.070| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.61 r_work: 0.3637 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8408 Z= 0.123 Angle : 0.545 11.818 11433 Z= 0.282 Chirality : 0.042 0.140 1356 Planarity : 0.003 0.036 1425 Dihedral : 6.352 79.396 1201 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.24 % Allowed : 18.89 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.02 (0.26), residues: 1074 helix: 1.22 (0.28), residues: 363 sheet: -0.18 (0.29), residues: 294 loop : -0.92 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.014 0.001 TYR E 178 PHE 0.022 0.001 PHE A 169 TRP 0.012 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8406) covalent geometry : angle 0.54373 (11429) SS BOND : bond 0.00327 ( 2) SS BOND : angle 1.75415 ( 4) hydrogen bonds : bond 0.04110 ( 414) hydrogen bonds : angle 4.83846 ( 1185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.204 Fit side-chains REVERT: A 151 MET cc_start: 0.7931 (mmm) cc_final: 0.7696 (tmm) REVERT: B 198 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8141 (tttm) outliers start: 19 outliers final: 15 residues processed: 171 average time/residue: 0.3701 time to fit residues: 68.1677 Evaluate side-chains 181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 38 optimal weight: 0.0970 chunk 18 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN C 268 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.142094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.127900 restraints weight = 11795.612| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.62 r_work: 0.3634 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8408 Z= 0.134 Angle : 0.549 12.599 11433 Z= 0.285 Chirality : 0.043 0.171 1356 Planarity : 0.003 0.036 1425 Dihedral : 6.346 77.869 1201 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.60 % Allowed : 19.36 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.01 (0.26), residues: 1074 helix: 1.22 (0.28), residues: 364 sheet: -0.15 (0.30), residues: 293 loop : -0.92 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.014 0.001 TYR E 178 PHE 0.021 0.001 PHE A 169 TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8406) covalent geometry : angle 0.54800 (11429) SS BOND : bond 0.00355 ( 2) SS BOND : angle 1.81327 ( 4) hydrogen bonds : bond 0.04163 ( 414) hydrogen bonds : angle 4.82681 ( 1185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.261 Fit side-chains REVERT: A 151 MET cc_start: 0.7955 (mmm) cc_final: 0.7718 (tmm) REVERT: B 198 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8283 (tttm) outliers start: 22 outliers final: 18 residues processed: 175 average time/residue: 0.4259 time to fit residues: 80.1500 Evaluate side-chains 188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.142892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.128521 restraints weight = 11765.172| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.63 r_work: 0.3643 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8408 Z= 0.120 Angle : 0.545 13.803 11433 Z= 0.281 Chirality : 0.042 0.167 1356 Planarity : 0.003 0.036 1425 Dihedral : 6.262 76.584 1201 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.13 % Allowed : 19.95 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.02 (0.26), residues: 1074 helix: 1.24 (0.28), residues: 366 sheet: -0.22 (0.30), residues: 283 loop : -0.89 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.014 0.001 TYR E 178 PHE 0.011 0.001 PHE A 314 TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8406) covalent geometry : angle 0.54392 (11429) SS BOND : bond 0.00334 ( 2) SS BOND : angle 1.63680 ( 4) hydrogen bonds : bond 0.04008 ( 414) hydrogen bonds : angle 4.78445 ( 1185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.297 Fit side-chains REVERT: A 151 MET cc_start: 0.7937 (mmm) cc_final: 0.7711 (mmm) REVERT: B 198 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8210 (tttm) REVERT: B 248 LEU cc_start: 0.8398 (mp) cc_final: 0.8191 (mp) REVERT: B 335 PHE cc_start: 0.8335 (t80) cc_final: 0.8037 (t80) outliers start: 18 outliers final: 15 residues processed: 172 average time/residue: 0.4409 time to fit residues: 81.7092 Evaluate side-chains 181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 96 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129518 restraints weight = 11720.107| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.66 r_work: 0.3619 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8408 Z= 0.169 Angle : 0.590 13.582 11433 Z= 0.304 Chirality : 0.044 0.181 1356 Planarity : 0.003 0.036 1425 Dihedral : 6.397 74.053 1201 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.36 % Allowed : 20.07 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.15 (0.26), residues: 1074 helix: 1.03 (0.27), residues: 368 sheet: -0.23 (0.29), residues: 293 loop : -0.94 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.028 0.002 TYR A 320 PHE 0.019 0.002 PHE A 70 TRP 0.012 0.001 TRP C 169 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8406) covalent geometry : angle 0.58914 (11429) SS BOND : bond 0.00395 ( 2) SS BOND : angle 2.09074 ( 4) hydrogen bonds : bond 0.04482 ( 414) hydrogen bonds : angle 4.93712 ( 1185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3115.57 seconds wall clock time: 53 minutes 44.13 seconds (3224.13 seconds total)