Starting phenix.real_space_refine on Fri Nov 15 15:21:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6o_35201/11_2024/8i6o_35201.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6o_35201/11_2024/8i6o_35201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6o_35201/11_2024/8i6o_35201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6o_35201/11_2024/8i6o_35201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6o_35201/11_2024/8i6o_35201.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6o_35201/11_2024/8i6o_35201.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.047 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 5876 2.51 5 N 1498 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9084 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2299 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 20} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2299 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 20} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 44 Chain: "E" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1126 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 148} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 12, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 64 Time building chain proxies: 6.03, per 1000 atoms: 0.66 Number of scatterers: 9084 At special positions: 0 Unit cell: (78.455, 81.77, 233.155, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1690 8.00 N 1498 7.00 C 5876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 961.6 milliseconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2186 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 61.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 removed outlier: 3.735A pdb=" N HIS A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 84 removed outlier: 3.887A pdb=" N SER A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 91 removed outlier: 4.407A pdb=" N TRP A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 129 through 142 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.673A pdb=" N GLU A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 234 removed outlier: 3.859A pdb=" N ARG A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG A 234 " --> pdb=" O HIS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 247 through 272 Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 273 through 293 removed outlier: 3.891A pdb=" N GLY A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 332 Processing helix chain 'B' and resid 41 through 49 removed outlier: 4.117A pdb=" N LEU B 45 " --> pdb=" O LYS B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.554A pdb=" N GLN B 80 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 81 " --> pdb=" O ARG B 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 77 through 81' Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.931A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.907A pdb=" N ILE B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 151 removed outlier: 4.036A pdb=" N ALA B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 186 removed outlier: 3.863A pdb=" N SER B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'C' and resid 36 through 54 Processing helix chain 'C' and resid 60 through 75 removed outlier: 3.748A pdb=" N GLY C 67 " --> pdb=" O CYS C 63 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU C 70 " --> pdb=" O MET C 66 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Proline residue: C 73 - end of helix Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 105 through 119 Processing helix chain 'C' and resid 129 through 140 removed outlier: 3.989A pdb=" N GLN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 180 removed outlier: 4.019A pdb=" N GLU C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 197 through 233 removed outlier: 3.547A pdb=" N LEU C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 202 " --> pdb=" O SER C 198 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 227 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 244 Processing helix chain 'C' and resid 247 through 292 removed outlier: 3.786A pdb=" N VAL C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) Proline residue: C 254 - end of helix removed outlier: 3.655A pdb=" N ASN C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY C 283 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASN C 287 " --> pdb=" O GLY C 283 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 313 Processing helix chain 'C' and resid 319 through 332 removed outlier: 3.938A pdb=" N ALA C 326 " --> pdb=" O TRP C 322 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N HIS C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 39 Processing helix chain 'D' and resid 40 through 49 removed outlier: 3.696A pdb=" N ILE D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 79 removed outlier: 3.576A pdb=" N ARG D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 101 through 108 Processing helix chain 'D' and resid 110 through 126 removed outlier: 3.710A pdb=" N GLU D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 124 " --> pdb=" O SER D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 151 removed outlier: 3.909A pdb=" N ALA D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 186 removed outlier: 4.077A pdb=" N GLU D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 removed outlier: 3.650A pdb=" N ALA D 201 " --> pdb=" O ALA D 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 98 removed outlier: 3.777A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN E 70 " --> pdb=" O ASP E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.765A pdb=" N GLN E 103 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.844A pdb=" N LEU E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 186 removed outlier: 3.992A pdb=" N ILE E 169 " --> pdb=" O VAL E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 200 removed outlier: 4.068A pdb=" N ALA E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN E 198 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN E 199 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97 removed outlier: 6.844A pdb=" N VAL A 158 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU A 127 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 160 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA A 125 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR A 162 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 21 removed outlier: 5.443A pdb=" N VAL B 7 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE B 4 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU B 60 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN B 6 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS B 58 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 83 removed outlier: 7.007A pdb=" N GLY B 82 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 211 removed outlier: 7.307A pdb=" N THR B 209 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.504A pdb=" N GLN C 126 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 186 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 8 removed outlier: 3.927A pdb=" N GLU D 5 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS D 58 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL D 7 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER D 56 " --> pdb=" O VAL D 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.652A pdb=" N PHE D 32 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 219 " --> pdb=" O MET D 207 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.657A pdb=" N ASP D 162 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA D 161 " --> pdb=" O LEU D 191 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2982 1.34 - 1.46: 1047 1.46 - 1.58: 5159 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 9226 Sorted by residual: bond pdb=" C ILE E 144 " pdb=" O ILE E 144 " ideal model delta sigma weight residual 1.237 1.220 0.017 1.29e-02 6.01e+03 1.82e+00 bond pdb=" CA GLU D 163 " pdb=" CB GLU D 163 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.33e+00 bond pdb=" CG GLU C 114 " pdb=" CD GLU C 114 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.27e+00 bond pdb=" CD GLU C 114 " pdb=" OE1 GLU C 114 " ideal model delta sigma weight residual 1.249 1.228 0.021 1.90e-02 2.77e+03 1.18e+00 bond pdb=" N LYS D 130 " pdb=" CA LYS D 130 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.40e-01 ... (remaining 9221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 12157 1.86 - 3.72: 239 3.72 - 5.57: 45 5.57 - 7.43: 8 7.43 - 9.29: 3 Bond angle restraints: 12452 Sorted by residual: angle pdb=" N VAL C 319 " pdb=" CA VAL C 319 " pdb=" C VAL C 319 " ideal model delta sigma weight residual 111.62 108.52 3.10 7.90e-01 1.60e+00 1.54e+01 angle pdb=" N GLU C 114 " pdb=" CA GLU C 114 " pdb=" CB GLU C 114 " ideal model delta sigma weight residual 110.28 116.11 -5.83 1.55e+00 4.16e-01 1.41e+01 angle pdb=" C ARG C 113 " pdb=" N GLU C 114 " pdb=" CA GLU C 114 " ideal model delta sigma weight residual 120.31 115.50 4.81 1.52e+00 4.33e-01 1.00e+01 angle pdb=" CB LYS E 173 " pdb=" CG LYS E 173 " pdb=" CD LYS E 173 " ideal model delta sigma weight residual 111.30 118.02 -6.72 2.30e+00 1.89e-01 8.53e+00 angle pdb=" N GLY C 58 " pdb=" CA GLY C 58 " pdb=" C GLY C 58 " ideal model delta sigma weight residual 111.10 107.05 4.05 1.46e+00 4.69e-01 7.70e+00 ... (remaining 12447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4961 17.96 - 35.92: 561 35.92 - 53.88: 87 53.88 - 71.84: 21 71.84 - 89.81: 8 Dihedral angle restraints: 5638 sinusoidal: 2242 harmonic: 3396 Sorted by residual: dihedral pdb=" CA LEU C 316 " pdb=" C LEU C 316 " pdb=" N GLY C 317 " pdb=" CA GLY C 317 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA PRO E 131 " pdb=" C PRO E 131 " pdb=" N GLU E 132 " pdb=" CA GLU E 132 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA HIS B 19 " pdb=" C HIS B 19 " pdb=" N GLU B 20 " pdb=" CA GLU B 20 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 951 0.032 - 0.063: 347 0.063 - 0.095: 126 0.095 - 0.127: 53 0.127 - 0.158: 5 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CB ILE E 169 " pdb=" CA ILE E 169 " pdb=" CG1 ILE E 169 " pdb=" CG2 ILE E 169 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CG LEU E 183 " pdb=" CB LEU E 183 " pdb=" CD1 LEU E 183 " pdb=" CD2 LEU E 183 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA GLN E 172 " pdb=" N GLN E 172 " pdb=" C GLN E 172 " pdb=" CB GLN E 172 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 1479 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 153 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO A 154 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 154 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 154 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 109 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO B 110 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 134 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO B 135 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 135 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 135 " -0.025 5.00e-02 4.00e+02 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 133 2.69 - 3.24: 9205 3.24 - 3.79: 13611 3.79 - 4.35: 16723 4.35 - 4.90: 26606 Nonbonded interactions: 66278 Sorted by model distance: nonbonded pdb=" O GLN E 151 " pdb=" OG SER E 154 " model vdw 2.135 3.040 nonbonded pdb=" OG SER C 105 " pdb=" OD1 ASN C 107 " model vdw 2.180 3.040 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG SER B 22 " model vdw 2.240 3.040 nonbonded pdb=" O ARG D 27 " pdb=" OG1 THR D 189 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP A 101 " pdb=" OG1 THR A 104 " model vdw 2.262 3.040 ... (remaining 66273 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.980 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 0.035 9226 Z= 0.185 Angle : 0.664 9.289 12452 Z= 0.348 Chirality : 0.041 0.158 1482 Planarity : 0.004 0.054 1559 Dihedral : 15.305 89.805 3452 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.61 % Allowed : 1.84 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1186 helix: 1.61 (0.21), residues: 696 sheet: -1.53 (0.67), residues: 66 loop : -2.34 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 90 HIS 0.007 0.001 HIS E 130 PHE 0.020 0.001 PHE E 155 TYR 0.014 0.001 TYR E 114 ARG 0.000 0.000 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8636 (m-30) cc_final: 0.8331 (m-30) REVERT: B 163 GLU cc_start: 0.8195 (tp30) cc_final: 0.7945 (tp30) REVERT: B 196 ASP cc_start: 0.8807 (t0) cc_final: 0.8122 (p0) REVERT: B 207 MET cc_start: 0.8162 (ptp) cc_final: 0.7544 (ptm) REVERT: B 209 THR cc_start: 0.8036 (m) cc_final: 0.7627 (t) REVERT: C 124 GLU cc_start: 0.8257 (pp20) cc_final: 0.8010 (pp20) REVERT: D 116 LYS cc_start: 0.8972 (ptpp) cc_final: 0.8756 (pttm) REVERT: D 169 ASP cc_start: 0.8462 (t0) cc_final: 0.8214 (t0) REVERT: E 169 ILE cc_start: 0.8959 (tp) cc_final: 0.8754 (tp) outliers start: 6 outliers final: 6 residues processed: 171 average time/residue: 0.2017 time to fit residues: 48.8777 Evaluate side-chains 133 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 194 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 HIS ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9226 Z= 0.236 Angle : 0.651 7.685 12452 Z= 0.332 Chirality : 0.041 0.140 1482 Planarity : 0.004 0.046 1559 Dihedral : 6.221 58.133 1234 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.05 % Allowed : 13.11 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1186 helix: 1.76 (0.21), residues: 705 sheet: -1.59 (0.66), residues: 64 loop : -2.52 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 318 HIS 0.008 0.001 HIS D 36 PHE 0.016 0.001 PHE E 155 TYR 0.011 0.001 TYR E 140 ARG 0.000 0.000 ARG E 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8073 (mmtp) REVERT: B 207 MET cc_start: 0.8339 (ptp) cc_final: 0.7626 (ptm) REVERT: B 209 THR cc_start: 0.8099 (m) cc_final: 0.7707 (t) REVERT: C 103 LYS cc_start: 0.7981 (tppt) cc_final: 0.7657 (pttt) REVERT: D 116 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8574 (pttm) REVERT: D 169 ASP cc_start: 0.8035 (t0) cc_final: 0.7630 (t0) REVERT: E 143 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6615 (t80) REVERT: E 169 ILE cc_start: 0.8992 (tp) cc_final: 0.8784 (tp) outliers start: 20 outliers final: 16 residues processed: 147 average time/residue: 0.2010 time to fit residues: 42.1073 Evaluate side-chains 145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 197 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9226 Z= 0.261 Angle : 0.643 8.659 12452 Z= 0.327 Chirality : 0.040 0.157 1482 Planarity : 0.004 0.047 1559 Dihedral : 5.687 58.807 1226 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.07 % Allowed : 18.24 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1186 helix: 1.73 (0.21), residues: 714 sheet: -1.97 (0.69), residues: 52 loop : -2.44 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 318 HIS 0.006 0.001 HIS D 88 PHE 0.018 0.001 PHE E 155 TYR 0.012 0.001 TYR E 114 ARG 0.000 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8225 (mmtm) cc_final: 0.7957 (mmtp) REVERT: B 191 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8469 (tt) REVERT: B 207 MET cc_start: 0.8461 (ptp) cc_final: 0.7878 (ptm) REVERT: B 209 THR cc_start: 0.8002 (m) cc_final: 0.7638 (t) REVERT: C 114 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8616 (mp0) REVERT: D 116 LYS cc_start: 0.8871 (ptpp) cc_final: 0.8567 (pttm) REVERT: D 144 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8520 (tm-30) REVERT: D 169 ASP cc_start: 0.8161 (t0) cc_final: 0.7752 (t0) REVERT: E 97 ASP cc_start: 0.9210 (m-30) cc_final: 0.8892 (m-30) REVERT: E 143 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6742 (t80) REVERT: E 169 ILE cc_start: 0.9050 (tp) cc_final: 0.8798 (tp) outliers start: 30 outliers final: 22 residues processed: 150 average time/residue: 0.2123 time to fit residues: 45.5905 Evaluate side-chains 152 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 151 GLN Chi-restraints excluded: chain E residue 197 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 0.0020 chunk 72 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9226 Z= 0.214 Angle : 0.614 7.496 12452 Z= 0.310 Chirality : 0.039 0.150 1482 Planarity : 0.004 0.047 1559 Dihedral : 5.336 51.697 1222 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.00 % Allowed : 20.29 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1186 helix: 1.82 (0.21), residues: 714 sheet: -1.85 (0.68), residues: 52 loop : -2.39 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 318 HIS 0.005 0.001 HIS D 88 PHE 0.009 0.001 PHE C 209 TYR 0.011 0.001 TYR E 114 ARG 0.000 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7920 (mmtp) REVERT: B 207 MET cc_start: 0.8339 (ptp) cc_final: 0.7749 (ptm) REVERT: B 209 THR cc_start: 0.7970 (m) cc_final: 0.7611 (t) REVERT: C 114 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8561 (mp0) REVERT: D 116 LYS cc_start: 0.8873 (ptpp) cc_final: 0.8608 (pttm) REVERT: D 144 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8395 (tm-30) REVERT: D 169 ASP cc_start: 0.8112 (t0) cc_final: 0.7696 (t0) REVERT: E 97 ASP cc_start: 0.9183 (OUTLIER) cc_final: 0.8714 (m-30) REVERT: E 143 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6785 (t80) REVERT: E 150 GLU cc_start: 0.8017 (tp30) cc_final: 0.7746 (tp30) REVERT: E 169 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8779 (tp) outliers start: 39 outliers final: 24 residues processed: 160 average time/residue: 0.1917 time to fit residues: 43.9892 Evaluate side-chains 156 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 197 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 103 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9226 Z= 0.207 Angle : 0.617 9.316 12452 Z= 0.309 Chirality : 0.039 0.151 1482 Planarity : 0.004 0.046 1559 Dihedral : 5.034 49.316 1218 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.79 % Allowed : 22.85 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1186 helix: 1.86 (0.21), residues: 716 sheet: -1.87 (0.68), residues: 52 loop : -2.39 (0.26), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 318 HIS 0.005 0.001 HIS C 41 PHE 0.008 0.001 PHE C 209 TYR 0.010 0.001 TYR E 114 ARG 0.000 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8167 (mmtm) cc_final: 0.7780 (mmtp) REVERT: B 207 MET cc_start: 0.8325 (ptp) cc_final: 0.7720 (ptm) REVERT: B 209 THR cc_start: 0.8116 (m) cc_final: 0.7703 (t) REVERT: C 114 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8528 (mp0) REVERT: C 258 MET cc_start: 0.7214 (ttm) cc_final: 0.6933 (ttm) REVERT: D 116 LYS cc_start: 0.8868 (ptpp) cc_final: 0.8597 (pttm) REVERT: D 144 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8435 (tm-30) REVERT: D 169 ASP cc_start: 0.8151 (t0) cc_final: 0.7759 (t0) REVERT: E 97 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8639 (m-30) REVERT: E 143 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6722 (t80) REVERT: E 150 GLU cc_start: 0.7923 (tp30) cc_final: 0.7634 (tp30) REVERT: E 169 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8718 (tp) outliers start: 37 outliers final: 26 residues processed: 153 average time/residue: 0.1975 time to fit residues: 43.3701 Evaluate side-chains 155 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain E residue 197 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 67 optimal weight: 0.0570 chunk 28 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9226 Z= 0.204 Angle : 0.635 11.400 12452 Z= 0.312 Chirality : 0.039 0.209 1482 Planarity : 0.004 0.046 1559 Dihedral : 4.723 47.307 1214 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.51 % Allowed : 23.67 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1186 helix: 1.93 (0.21), residues: 715 sheet: -1.84 (0.67), residues: 52 loop : -2.36 (0.26), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 318 HIS 0.008 0.001 HIS C 230 PHE 0.008 0.001 PHE C 209 TYR 0.011 0.001 TYR E 140 ARG 0.000 0.000 ARG E 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7731 (mmtp) REVERT: B 144 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8048 (pp30) REVERT: B 207 MET cc_start: 0.8309 (ptp) cc_final: 0.7663 (ptm) REVERT: B 209 THR cc_start: 0.8150 (m) cc_final: 0.7743 (t) REVERT: C 114 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8599 (mp0) REVERT: C 167 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7656 (p0) REVERT: C 258 MET cc_start: 0.7194 (ttm) cc_final: 0.6928 (ttm) REVERT: D 116 LYS cc_start: 0.8880 (ptpp) cc_final: 0.8626 (pttm) REVERT: D 169 ASP cc_start: 0.8123 (t0) cc_final: 0.7740 (t0) REVERT: E 97 ASP cc_start: 0.9132 (OUTLIER) cc_final: 0.8629 (m-30) REVERT: E 143 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.6865 (t80) REVERT: E 150 GLU cc_start: 0.7916 (tp30) cc_final: 0.7634 (tp30) REVERT: E 169 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8768 (tp) outliers start: 44 outliers final: 26 residues processed: 158 average time/residue: 0.1966 time to fit residues: 44.9564 Evaluate side-chains 157 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 172 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 HIS D 126 ASN E 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9226 Z= 0.212 Angle : 0.637 11.282 12452 Z= 0.315 Chirality : 0.039 0.182 1482 Planarity : 0.004 0.046 1559 Dihedral : 4.690 44.822 1214 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.51 % Allowed : 23.98 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1186 helix: 1.92 (0.21), residues: 717 sheet: -1.82 (0.67), residues: 52 loop : -2.39 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 90 HIS 0.004 0.001 HIS C 41 PHE 0.014 0.001 PHE E 155 TYR 0.010 0.001 TYR E 140 ARG 0.000 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8010 (pp30) REVERT: B 207 MET cc_start: 0.8306 (ptp) cc_final: 0.7523 (ptm) REVERT: B 209 THR cc_start: 0.8086 (m) cc_final: 0.7696 (t) REVERT: C 114 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8547 (mp0) REVERT: C 167 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7686 (p0) REVERT: C 258 MET cc_start: 0.7201 (ttm) cc_final: 0.6929 (ttm) REVERT: D 116 LYS cc_start: 0.8891 (ptpp) cc_final: 0.8635 (pttm) REVERT: D 169 ASP cc_start: 0.8136 (t0) cc_final: 0.7703 (t0) REVERT: E 97 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8665 (m-30) REVERT: E 143 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.6835 (t80) REVERT: E 150 GLU cc_start: 0.7939 (tp30) cc_final: 0.7647 (tp30) REVERT: E 169 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8787 (tp) outliers start: 44 outliers final: 32 residues processed: 155 average time/residue: 0.2051 time to fit residues: 45.1655 Evaluate side-chains 164 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 172 GLN Chi-restraints excluded: chain E residue 197 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9226 Z= 0.198 Angle : 0.637 10.636 12452 Z= 0.315 Chirality : 0.039 0.175 1482 Planarity : 0.004 0.046 1559 Dihedral : 4.672 42.867 1214 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.30 % Allowed : 24.49 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1186 helix: 1.95 (0.21), residues: 715 sheet: -1.74 (0.68), residues: 52 loop : -2.36 (0.26), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 90 HIS 0.006 0.001 HIS C 230 PHE 0.013 0.001 PHE E 155 TYR 0.010 0.001 TYR E 140 ARG 0.000 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8338 (mmpt) cc_final: 0.8018 (mmtp) REVERT: B 144 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7982 (pp30) REVERT: B 207 MET cc_start: 0.8282 (ptp) cc_final: 0.7638 (ptm) REVERT: B 209 THR cc_start: 0.8141 (m) cc_final: 0.7747 (t) REVERT: C 114 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: C 167 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7633 (p0) REVERT: C 258 MET cc_start: 0.7126 (ttm) cc_final: 0.6859 (ttm) REVERT: D 9 LYS cc_start: 0.7698 (tttt) cc_final: 0.7497 (tmtt) REVERT: D 116 LYS cc_start: 0.8890 (ptpp) cc_final: 0.8630 (pttm) REVERT: D 169 ASP cc_start: 0.8109 (t0) cc_final: 0.7684 (t0) REVERT: E 97 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8659 (m-30) REVERT: E 143 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6840 (t80) REVERT: E 150 GLU cc_start: 0.7931 (tp30) cc_final: 0.7639 (tp30) REVERT: E 179 LYS cc_start: 0.6082 (pttt) cc_final: 0.5866 (pptt) outliers start: 42 outliers final: 29 residues processed: 155 average time/residue: 0.2011 time to fit residues: 44.3939 Evaluate side-chains 156 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 172 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9226 Z= 0.254 Angle : 0.677 12.367 12452 Z= 0.334 Chirality : 0.040 0.240 1482 Planarity : 0.004 0.045 1559 Dihedral : 4.719 39.583 1214 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.20 % Allowed : 24.90 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1186 helix: 1.83 (0.20), residues: 716 sheet: -2.01 (0.63), residues: 57 loop : -2.42 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 90 HIS 0.011 0.001 HIS C 230 PHE 0.026 0.001 PHE E 155 TYR 0.011 0.001 TYR E 140 ARG 0.000 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 LYS cc_start: 0.8336 (mmpt) cc_final: 0.7953 (mmtp) REVERT: B 144 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8033 (pp30) REVERT: B 196 ASP cc_start: 0.8750 (t0) cc_final: 0.7927 (p0) REVERT: B 207 MET cc_start: 0.8331 (ptp) cc_final: 0.7441 (ptm) REVERT: B 209 THR cc_start: 0.8086 (m) cc_final: 0.7712 (t) REVERT: C 114 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8600 (mp0) REVERT: C 167 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7621 (p0) REVERT: C 258 MET cc_start: 0.7177 (ttm) cc_final: 0.6886 (ttm) REVERT: D 116 LYS cc_start: 0.8915 (ptpp) cc_final: 0.8645 (pttm) REVERT: D 169 ASP cc_start: 0.8187 (t0) cc_final: 0.7777 (t0) REVERT: E 93 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8691 (mmmt) REVERT: E 97 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8669 (m-30) REVERT: E 143 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6867 (t80) REVERT: E 150 GLU cc_start: 0.7985 (tp30) cc_final: 0.7677 (tp30) outliers start: 41 outliers final: 33 residues processed: 159 average time/residue: 0.1941 time to fit residues: 43.9636 Evaluate side-chains 165 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 197 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.5980 chunk 78 optimal weight: 0.0570 chunk 118 optimal weight: 0.4980 chunk 109 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 74 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 HIS D 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9226 Z= 0.196 Angle : 0.694 16.337 12452 Z= 0.341 Chirality : 0.041 0.236 1482 Planarity : 0.004 0.046 1559 Dihedral : 4.722 37.451 1214 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.59 % Allowed : 25.82 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1186 helix: 1.90 (0.21), residues: 716 sheet: -1.70 (0.68), residues: 52 loop : -2.45 (0.26), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 90 HIS 0.005 0.001 HIS C 41 PHE 0.031 0.001 PHE E 155 TYR 0.034 0.001 TYR E 140 ARG 0.000 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 LEU cc_start: 0.8126 (mm) cc_final: 0.7816 (mm) REVERT: B 144 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8065 (pp30) REVERT: B 196 ASP cc_start: 0.8498 (t0) cc_final: 0.8247 (t0) REVERT: B 207 MET cc_start: 0.8226 (ptp) cc_final: 0.7594 (ptm) REVERT: B 209 THR cc_start: 0.8084 (m) cc_final: 0.7667 (t) REVERT: C 103 LYS cc_start: 0.7991 (tppt) cc_final: 0.7562 (pttt) REVERT: C 114 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8649 (mp0) REVERT: C 167 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7608 (p0) REVERT: C 258 MET cc_start: 0.7001 (ttm) cc_final: 0.6732 (ttm) REVERT: D 109 MET cc_start: 0.6719 (mmt) cc_final: 0.6441 (mmt) REVERT: D 116 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8676 (pttm) REVERT: D 169 ASP cc_start: 0.8114 (t0) cc_final: 0.7721 (t0) REVERT: E 93 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8692 (mmmt) REVERT: E 97 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8712 (m-30) REVERT: E 143 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6864 (t80) REVERT: E 150 GLU cc_start: 0.7961 (tp30) cc_final: 0.7636 (tp30) outliers start: 35 outliers final: 27 residues processed: 153 average time/residue: 0.2093 time to fit residues: 45.7649 Evaluate side-chains 160 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 HIS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 118 ARG Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 143 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 94 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 HIS D 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.135684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099445 restraints weight = 20476.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.099392 restraints weight = 11279.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.100531 restraints weight = 8380.193| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9226 Z= 0.202 Angle : 0.688 12.558 12452 Z= 0.338 Chirality : 0.041 0.244 1482 Planarity : 0.004 0.047 1559 Dihedral : 4.659 36.320 1214 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.38 % Allowed : 26.23 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1186 helix: 1.90 (0.21), residues: 717 sheet: -1.65 (0.68), residues: 52 loop : -2.46 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 90 HIS 0.005 0.001 HIS C 41 PHE 0.029 0.001 PHE E 155 TYR 0.017 0.001 TYR E 140 ARG 0.000 0.000 ARG E 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.52 seconds wall clock time: 38 minutes 57.38 seconds (2337.38 seconds total)