Starting phenix.real_space_refine on Sun Apr 5 03:40:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ppw_71776/04_2026/9ppw_71776_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ppw_71776/04_2026/9ppw_71776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ppw_71776/04_2026/9ppw_71776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ppw_71776/04_2026/9ppw_71776.map" model { file = "/net/cci-nas-00/data/ceres_data/9ppw_71776/04_2026/9ppw_71776_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ppw_71776/04_2026/9ppw_71776_neut.cif" } resolution = 3.32 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= 0.021 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 55 5.16 5 C 5017 2.51 5 N 1340 2.21 5 O 1408 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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7820 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 1844 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 12, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 299 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'TYR:plan': 5, 'PHE:plan': 3, 'ARG:plan': 11, 'ASP:plan': 7, 'GLU:plan': 3, 'GLN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 171 Chain: "B" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1505 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2423 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain breaks: 2 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 9, 'GLN:plan1': 3, 'ARG:plan': 8, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 108 Chain: "D" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 340 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1677 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'EJ4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.92, per 1000 atoms: 0.25 Number of scatterers: 7820 At special positions: 0 Unit cell: (89.76, 124.08, 125.84, 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 55 16.00 O 1408 8.00 N 1340 7.00 C 5017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 385.6 milliseconds 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: 2060 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 13 sheets defined 35.7% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 48 through 77 removed outlier: 4.029A pdb=" N THR A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 102 Processing helix chain 'A' and resid 102 through 112 removed outlier: 4.064A pdb=" N SER A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 152 removed outlier: 3.701A pdb=" N LEU A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 161 through 186 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 208 through 241 removed outlier: 3.782A pdb=" N ALA A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 255 through 285 Proline residue: A 276 - end of helix removed outlier: 3.853A pdb=" N ILE A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 322 removed outlier: 3.701A pdb=" N VAL A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Proline residue: A 315 - end of helix removed outlier: 3.599A pdb=" N ASP A 322 " --> pdb=" O TYR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.571A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.536A pdb=" N ALA B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'D' and resid 12 through 22 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.724A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 208 through 212 removed outlier: 4.010A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.530A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 60 through 63 removed outlier: 3.611A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.009A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.148A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.930A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.478A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.617A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.769A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.943A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.943A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136 removed outlier: 3.593A pdb=" N TYR E 215 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1212 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: 1.34 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1262 1.31 - 1.43: 2179 1.43 - 1.56: 4462 1.56 - 1.69: 6 1.69 - 1.82: 79 Bond restraints: 7988 Sorted by residual: bond pdb=" CBB EJ4 A 401 " pdb=" NAS EJ4 A 401 " ideal model delta sigma weight residual 1.452 1.178 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" CAU EJ4 A 401 " pdb=" CAV EJ4 A 401 " ideal model delta sigma weight residual 1.536 1.350 0.186 2.00e-02 2.50e+03 8.67e+01 bond pdb=" CAC EJ4 A 401 " pdb=" OAD EJ4 A 401 " ideal model delta sigma weight residual 1.359 1.543 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" CAT EJ4 A 401 " pdb=" CAU EJ4 A 401 " ideal model delta sigma weight residual 1.522 1.633 -0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" CAX EJ4 A 401 " pdb=" CBA EJ4 A 401 " ideal model delta sigma weight residual 1.505 1.611 -0.106 2.00e-02 2.50e+03 2.79e+01 ... (remaining 7983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 10627 1.67 - 3.33: 246 3.33 - 5.00: 36 5.00 - 6.67: 11 6.67 - 8.34: 4 Bond angle restraints: 10924 Sorted by residual: angle pdb=" N GLU A 251 " pdb=" CA GLU A 251 " pdb=" C GLU A 251 " ideal model delta sigma weight residual 114.04 109.77 4.27 1.24e+00 6.50e-01 1.18e+01 angle pdb=" CAB EJ4 A 401 " pdb=" CAC EJ4 A 401 " pdb=" OAD EJ4 A 401 " ideal model delta sigma weight residual 127.18 135.52 -8.34 3.00e+00 1.11e-01 7.72e+00 angle pdb=" N PRO C 236 " pdb=" CA PRO C 236 " pdb=" C PRO C 236 " ideal model delta sigma weight residual 113.65 117.17 -3.52 1.35e+00 5.49e-01 6.81e+00 angle pdb=" CD ARG C 134 " pdb=" NE ARG C 134 " pdb=" CZ ARG C 134 " ideal model delta sigma weight residual 124.40 127.95 -3.55 1.40e+00 5.10e-01 6.44e+00 angle pdb=" CA ILE C 93 " pdb=" CB ILE C 93 " pdb=" CG1 ILE C 93 " ideal model delta sigma weight residual 110.40 114.69 -4.29 1.70e+00 3.46e-01 6.37e+00 ... (remaining 10919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 4065 17.21 - 34.41: 434 34.41 - 51.62: 141 51.62 - 68.82: 27 68.82 - 86.03: 5 Dihedral angle restraints: 4672 sinusoidal: 1491 harmonic: 3181 Sorted by residual: dihedral pdb=" CA ASP C 291 " pdb=" C ASP C 291 " pdb=" N PHE C 292 " pdb=" CA PHE C 292 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 4669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1084 0.058 - 0.116: 187 0.116 - 0.175: 24 0.175 - 0.233: 3 0.233 - 0.291: 1 Chirality restraints: 1299 Sorted by residual: chirality pdb=" CBC EJ4 A 401 " pdb=" CBB EJ4 A 401 " pdb=" CBD EJ4 A 401 " pdb=" CBE EJ4 A 401 " both_signs ideal model delta sigma weight residual True 2.43 -2.72 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CAR EJ4 A 401 " pdb=" CAP EJ4 A 401 " pdb=" CBA EJ4 A 401 " pdb=" NAS EJ4 A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CAP EJ4 A 401 " pdb=" CAO EJ4 A 401 " pdb=" CAR EJ4 A 401 " pdb=" CAV EJ4 A 401 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 1296 not shown) Planarity restraints: 1387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO C 236 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 274 " -0.014 2.00e-02 2.50e+03 2.02e-02 7.14e+00 pdb=" CG PHE B 274 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 274 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 274 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE B 274 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 274 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 274 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 199 " -0.009 2.00e-02 2.50e+03 1.05e-02 1.93e+00 pdb=" CG PHE B 199 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 199 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 199 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 199 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 199 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 199 " -0.001 2.00e-02 2.50e+03 ... (remaining 1384 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 620 2.74 - 3.28: 7384 3.28 - 3.82: 13244 3.82 - 4.36: 14774 4.36 - 4.90: 26827 Nonbonded interactions: 62849 Sorted by model distance: nonbonded pdb=" O SER E 181 " pdb=" ND2 ASN E 182 " model vdw 2.198 3.120 nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.223 3.040 nonbonded pdb=" O SER E 106 " pdb=" OG SER E 106 " model vdw 2.231 3.040 nonbonded pdb=" OG SER C 67 " pdb=" OD1 ASP C 323 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.244 3.040 ... (remaining 62844 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: 1.550 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 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 : 0.007 0.274 7990 Z= 0.314 Angle : 0.639 8.337 10928 Z= 0.339 Chirality : 0.046 0.291 1299 Planarity : 0.004 0.070 1387 Dihedral : 16.554 86.030 2606 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.58 % Allowed : 33.53 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.25), residues: 1074 helix: 1.66 (0.27), residues: 363 sheet: -0.16 (0.31), residues: 275 loop : -1.36 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 98 TYR 0.016 0.002 TYR C 145 PHE 0.046 0.002 PHE B 274 TRP 0.022 0.002 TRP C 211 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00653 ( 7988) covalent geometry : angle 0.63775 (10924) SS BOND : bond 0.00151 ( 2) SS BOND : angle 2.21252 ( 4) hydrogen bonds : bond 0.12186 ( 428) hydrogen bonds : angle 5.77818 ( 1212) *********************** 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 170 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 164 average time/residue: 0.0845 time to fit residues: 18.8502 Evaluate side-chains 136 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain C residue 317 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 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 90 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN C 220 GLN D 59 ASN E 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.144906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129324 restraints weight = 11531.572| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.39 r_work: 0.3579 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 7990 Z= 0.221 Angle : 0.704 11.316 10928 Z= 0.376 Chirality : 0.047 0.171 1299 Planarity : 0.005 0.064 1387 Dihedral : 5.391 40.289 1210 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.61 % Allowed : 28.35 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.25), residues: 1074 helix: 1.67 (0.27), residues: 369 sheet: 0.31 (0.32), residues: 269 loop : -1.48 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 304 TYR 0.021 0.003 TYR B 290 PHE 0.064 0.004 PHE E 32 TRP 0.026 0.004 TRP C 211 HIS 0.014 0.002 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 7988) covalent geometry : angle 0.70252 (10924) SS BOND : bond 0.00195 ( 2) SS BOND : angle 2.52306 ( 4) hydrogen bonds : bond 0.04159 ( 428) hydrogen bonds : angle 4.84888 ( 1212) *********************** 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 185 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 280 PHE cc_start: 0.4198 (OUTLIER) cc_final: 0.3791 (t80) REVERT: B 10 LYS cc_start: 0.8298 (ttmt) cc_final: 0.8076 (mtmm) REVERT: B 297 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5625 (mp0) REVERT: C 61 MET cc_start: 0.7228 (ppp) cc_final: 0.6933 (ppp) REVERT: C 262 MET cc_start: 0.7054 (tpp) cc_final: 0.6692 (tpp) outliers start: 39 outliers final: 18 residues processed: 172 average time/residue: 0.0797 time to fit residues: 18.7654 Evaluate side-chains 153 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain E residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 0.0030 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 119 ASN C 176 GLN E 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124531 restraints weight = 11181.241| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.40 r_work: 0.3506 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.6654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7990 Z= 0.157 Angle : 0.564 6.963 10928 Z= 0.301 Chirality : 0.042 0.147 1299 Planarity : 0.004 0.065 1387 Dihedral : 4.601 39.751 1207 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.89 % Allowed : 28.92 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1074 helix: 2.20 (0.27), residues: 364 sheet: 0.18 (0.31), residues: 276 loop : -1.41 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 134 TYR 0.014 0.002 TYR C 145 PHE 0.023 0.002 PHE C 199 TRP 0.023 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7988) covalent geometry : angle 0.56374 (10924) SS BOND : bond 0.00134 ( 2) SS BOND : angle 1.56975 ( 4) hydrogen bonds : bond 0.04063 ( 428) hydrogen bonds : angle 4.45294 ( 1212) *********************** 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 171 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.282 Fit side-chains REVERT: A 231 VAL cc_start: 0.7262 (t) cc_final: 0.6935 (p) REVERT: B 10 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8100 (mtmm) REVERT: B 18 MET cc_start: 0.7681 (tpp) cc_final: 0.7313 (tpp) REVERT: C 61 MET cc_start: 0.7706 (ppp) cc_final: 0.7057 (ppp) REVERT: C 219 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7295 (mtp-110) REVERT: C 262 MET cc_start: 0.7184 (tpp) cc_final: 0.6595 (tpp) REVERT: E 219 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6873 (pt0) outliers start: 34 outliers final: 11 residues processed: 156 average time/residue: 0.0912 time to fit residues: 19.1320 Evaluate side-chains 146 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 219 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 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 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123270 restraints weight = 11370.235| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.52 r_work: 0.3474 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.7487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7990 Z= 0.149 Angle : 0.544 8.648 10928 Z= 0.290 Chirality : 0.042 0.142 1299 Planarity : 0.004 0.064 1387 Dihedral : 4.493 36.005 1206 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.32 % Allowed : 28.49 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 1074 helix: 2.38 (0.27), residues: 365 sheet: 0.31 (0.31), residues: 263 loop : -1.42 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 32 TYR 0.010 0.001 TYR E 95 PHE 0.017 0.002 PHE C 199 TRP 0.019 0.002 TRP C 211 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7988) covalent geometry : angle 0.54191 (10924) SS BOND : bond 0.00301 ( 2) SS BOND : angle 2.27324 ( 4) hydrogen bonds : bond 0.03636 ( 428) hydrogen bonds : angle 4.39756 ( 1212) *********************** 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 171 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.280 Fit side-chains REVERT: A 186 MET cc_start: 0.4666 (tmm) cc_final: 0.4388 (mtp) REVERT: A 240 LEU cc_start: 0.8449 (mt) cc_final: 0.8214 (mp) REVERT: A 280 PHE cc_start: 0.5120 (OUTLIER) cc_final: 0.4562 (t80) REVERT: B 10 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8119 (mtmm) REVERT: B 18 MET cc_start: 0.7796 (tpp) cc_final: 0.7359 (ttm) REVERT: B 354 PHE cc_start: 0.5086 (OUTLIER) cc_final: 0.4462 (t80) REVERT: C 61 MET cc_start: 0.7796 (ppp) cc_final: 0.7465 (ppp) REVERT: C 262 MET cc_start: 0.7040 (tpp) cc_final: 0.6513 (tpp) REVERT: C 315 VAL cc_start: 0.7690 (m) cc_final: 0.7352 (t) REVERT: E 22 CYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6749 (t) REVERT: E 219 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6919 (pt0) outliers start: 30 outliers final: 15 residues processed: 162 average time/residue: 0.0950 time to fit residues: 20.5608 Evaluate side-chains 157 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 219 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.6980 chunk 15 optimal weight: 0.0470 chunk 107 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 23 optimal weight: 0.0040 chunk 99 optimal weight: 1.9990 overall best weight: 0.4890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123380 restraints weight = 11247.595| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.52 r_work: 0.3474 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.7904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7990 Z= 0.125 Angle : 0.508 7.414 10928 Z= 0.271 Chirality : 0.041 0.136 1299 Planarity : 0.004 0.065 1387 Dihedral : 4.285 37.453 1206 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.75 % Allowed : 28.06 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.26), residues: 1074 helix: 2.56 (0.27), residues: 365 sheet: 0.27 (0.31), residues: 268 loop : -1.36 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 134 TYR 0.014 0.001 TYR E 50 PHE 0.016 0.001 PHE C 199 TRP 0.017 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7988) covalent geometry : angle 0.50687 (10924) SS BOND : bond 0.00690 ( 2) SS BOND : angle 1.99383 ( 4) hydrogen bonds : bond 0.03446 ( 428) hydrogen bonds : angle 4.21936 ( 1212) *********************** 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 172 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.272 Fit side-chains REVERT: A 240 LEU cc_start: 0.8434 (mt) cc_final: 0.8227 (mp) REVERT: A 280 PHE cc_start: 0.4997 (OUTLIER) cc_final: 0.4348 (t80) REVERT: B 18 MET cc_start: 0.7739 (tpp) cc_final: 0.7351 (ttm) REVERT: B 199 PHE cc_start: 0.7690 (m-80) cc_final: 0.7382 (m-80) REVERT: B 354 PHE cc_start: 0.4977 (OUTLIER) cc_final: 0.4315 (t80) REVERT: C 234 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: C 246 ASP cc_start: 0.7527 (t70) cc_final: 0.7163 (m-30) REVERT: C 262 MET cc_start: 0.7078 (tpp) cc_final: 0.6688 (tpp) REVERT: C 315 VAL cc_start: 0.7709 (m) cc_final: 0.7369 (t) REVERT: D 38 MET cc_start: 0.7269 (ttm) cc_final: 0.6987 (ttm) REVERT: E 22 CYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6659 (t) REVERT: E 219 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6960 (pt0) outliers start: 33 outliers final: 19 residues processed: 162 average time/residue: 0.0823 time to fit residues: 18.2577 Evaluate side-chains 161 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 219 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.0060 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122023 restraints weight = 11289.927| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.38 r_work: 0.3466 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.8387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7990 Z= 0.155 Angle : 0.538 7.343 10928 Z= 0.286 Chirality : 0.042 0.141 1299 Planarity : 0.004 0.065 1387 Dihedral : 4.494 37.167 1206 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.32 % Allowed : 27.34 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1074 helix: 2.46 (0.27), residues: 367 sheet: 0.36 (0.31), residues: 265 loop : -1.40 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 134 TYR 0.012 0.002 TYR E 50 PHE 0.019 0.002 PHE C 199 TRP 0.021 0.002 TRP C 211 HIS 0.004 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7988) covalent geometry : angle 0.53675 (10924) SS BOND : bond 0.00229 ( 2) SS BOND : angle 2.02792 ( 4) hydrogen bonds : bond 0.03761 ( 428) hydrogen bonds : angle 4.31281 ( 1212) *********************** 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 181 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.226 Fit side-chains REVERT: A 280 PHE cc_start: 0.4977 (OUTLIER) cc_final: 0.4258 (t80) REVERT: B 18 MET cc_start: 0.7753 (tpp) cc_final: 0.7398 (ttm) REVERT: B 199 PHE cc_start: 0.7666 (m-80) cc_final: 0.7438 (m-80) REVERT: B 354 PHE cc_start: 0.4911 (OUTLIER) cc_final: 0.4219 (t80) REVERT: C 111 TYR cc_start: 0.8183 (m-80) cc_final: 0.7928 (m-80) REVERT: C 234 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: C 246 ASP cc_start: 0.7471 (t70) cc_final: 0.7089 (t0) REVERT: C 262 MET cc_start: 0.6981 (tpp) cc_final: 0.6432 (tpp) REVERT: D 38 MET cc_start: 0.7456 (ttm) cc_final: 0.7186 (ttm) REVERT: E 22 CYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6690 (t) REVERT: E 214 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7585 (m) REVERT: E 219 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.7028 (pt0) outliers start: 37 outliers final: 25 residues processed: 172 average time/residue: 0.0826 time to fit residues: 19.5113 Evaluate side-chains 170 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 219 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 0.0370 chunk 6 optimal weight: 0.0020 chunk 100 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 overall best weight: 0.2466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124982 restraints weight = 11286.596| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.40 r_work: 0.3504 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.8510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7990 Z= 0.097 Angle : 0.512 15.967 10928 Z= 0.266 Chirality : 0.040 0.134 1299 Planarity : 0.003 0.064 1387 Dihedral : 4.131 37.068 1206 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.75 % Allowed : 27.34 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.26), residues: 1074 helix: 2.74 (0.28), residues: 366 sheet: 0.54 (0.32), residues: 257 loop : -1.40 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.012 0.001 TYR A 130 PHE 0.012 0.001 PHE C 241 TRP 0.018 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 7988) covalent geometry : angle 0.50944 (10924) SS BOND : bond 0.00305 ( 2) SS BOND : angle 2.65324 ( 4) hydrogen bonds : bond 0.03132 ( 428) hydrogen bonds : angle 4.08124 ( 1212) *********************** 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 176 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.265 Fit side-chains REVERT: A 280 PHE cc_start: 0.5028 (OUTLIER) cc_final: 0.4348 (t80) REVERT: B 18 MET cc_start: 0.7720 (tpp) cc_final: 0.7445 (ttm) REVERT: B 354 PHE cc_start: 0.4804 (OUTLIER) cc_final: 0.4110 (t80) REVERT: C 234 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: C 246 ASP cc_start: 0.7454 (t70) cc_final: 0.7027 (t0) REVERT: D 38 MET cc_start: 0.7391 (ttm) cc_final: 0.7160 (ttm) REVERT: E 22 CYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6561 (t) REVERT: E 219 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6951 (pt0) outliers start: 33 outliers final: 19 residues processed: 167 average time/residue: 0.0879 time to fit residues: 19.8055 Evaluate side-chains 162 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 284 TRP Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 219 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.137927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121506 restraints weight = 11305.477| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.41 r_work: 0.3451 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.8702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7990 Z= 0.178 Angle : 0.565 9.628 10928 Z= 0.297 Chirality : 0.043 0.165 1299 Planarity : 0.004 0.064 1387 Dihedral : 4.445 37.855 1206 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.60 % Allowed : 28.20 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1074 helix: 2.50 (0.27), residues: 368 sheet: 0.34 (0.32), residues: 267 loop : -1.37 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 150 TYR 0.014 0.002 TYR E 50 PHE 0.022 0.002 PHE C 199 TRP 0.021 0.002 TRP C 211 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 7988) covalent geometry : angle 0.56040 (10924) SS BOND : bond 0.00342 ( 2) SS BOND : angle 3.85274 ( 4) hydrogen bonds : bond 0.03853 ( 428) hydrogen bonds : angle 4.29262 ( 1212) *********************** 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 172 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.289 Fit side-chains REVERT: A 280 PHE cc_start: 0.5054 (OUTLIER) cc_final: 0.4348 (t80) REVERT: B 18 MET cc_start: 0.7723 (tpp) cc_final: 0.7387 (ttm) REVERT: C 111 TYR cc_start: 0.8163 (m-80) cc_final: 0.7903 (m-80) REVERT: C 234 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: D 38 MET cc_start: 0.7507 (ttm) cc_final: 0.7256 (ttm) REVERT: D 60 PRO cc_start: 0.8403 (Cg_endo) cc_final: 0.8124 (Cg_exo) REVERT: E 22 CYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6679 (t) REVERT: E 214 VAL cc_start: 0.7845 (OUTLIER) cc_final: 0.7601 (m) REVERT: E 219 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7011 (pt0) outliers start: 32 outliers final: 23 residues processed: 161 average time/residue: 0.0863 time to fit residues: 18.7790 Evaluate side-chains 167 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 PHE Chi-restraints excluded: chain A residue 284 TRP Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 219 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 90 optimal weight: 0.0040 chunk 10 optimal weight: 0.0370 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.136106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120114 restraints weight = 11410.156| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.41 r_work: 0.3440 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.8967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7990 Z= 0.183 Angle : 0.569 6.137 10928 Z= 0.302 Chirality : 0.043 0.151 1299 Planarity : 0.004 0.065 1387 Dihedral : 4.579 39.010 1206 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 5.04 % Allowed : 26.91 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 1074 helix: 2.33 (0.27), residues: 367 sheet: 0.27 (0.31), residues: 273 loop : -1.44 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 146 TYR 0.016 0.002 TYR E 50 PHE 0.021 0.002 PHE C 199 TRP 0.021 0.002 TRP C 211 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 7988) covalent geometry : angle 0.56549 (10924) SS BOND : bond 0.00264 ( 2) SS BOND : angle 3.49666 ( 4) hydrogen bonds : bond 0.04007 ( 428) hydrogen bonds : angle 4.39687 ( 1212) *********************** 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 172 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.269 Fit side-chains REVERT: B 18 MET cc_start: 0.7666 (tpp) cc_final: 0.7340 (ttm) REVERT: C 101 MET cc_start: 0.7122 (mpp) cc_final: 0.6918 (mtm) REVERT: C 234 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7793 (m-80) REVERT: D 60 PRO cc_start: 0.8437 (Cg_endo) cc_final: 0.8178 (Cg_exo) REVERT: E 22 CYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6795 (t) REVERT: E 214 VAL cc_start: 0.7885 (OUTLIER) cc_final: 0.7645 (m) REVERT: E 219 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6981 (pt0) outliers start: 35 outliers final: 22 residues processed: 161 average time/residue: 0.0877 time to fit residues: 19.1414 Evaluate side-chains 161 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 284 TRP Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 219 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 56 optimal weight: 0.0670 chunk 0 optimal weight: 4.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120041 restraints weight = 11338.363| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.40 r_work: 0.3440 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.9090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7990 Z= 0.174 Angle : 0.577 13.362 10928 Z= 0.303 Chirality : 0.043 0.148 1299 Planarity : 0.004 0.065 1387 Dihedral : 4.531 39.295 1206 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 4.75 % Allowed : 26.76 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 1074 helix: 2.34 (0.27), residues: 367 sheet: 0.25 (0.31), residues: 273 loop : -1.44 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 134 TYR 0.014 0.002 TYR E 50 PHE 0.021 0.002 PHE C 199 TRP 0.019 0.002 TRP C 211 HIS 0.003 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7988) covalent geometry : angle 0.57435 (10924) SS BOND : bond 0.00258 ( 2) SS BOND : angle 3.19492 ( 4) hydrogen bonds : bond 0.03944 ( 428) hydrogen bonds : angle 4.38127 ( 1212) ********************** 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 170 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.256 Fit side-chains REVERT: A 186 MET cc_start: 0.5270 (tmm) cc_final: 0.4408 (mtp) REVERT: B 18 MET cc_start: 0.7659 (tpp) cc_final: 0.7099 (mpp) REVERT: C 17 GLN cc_start: 0.6329 (OUTLIER) cc_final: 0.5973 (tp40) REVERT: C 101 MET cc_start: 0.7177 (mpp) cc_final: 0.6929 (mtm) REVERT: C 234 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: E 22 CYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6780 (t) REVERT: E 214 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7624 (m) REVERT: E 219 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.7010 (pt0) outliers start: 33 outliers final: 23 residues processed: 161 average time/residue: 0.0870 time to fit residues: 19.0145 Evaluate side-chains 164 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 284 TRP Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 219 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS B 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120934 restraints weight = 11257.710| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.40 r_work: 0.3454 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.9170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7990 Z= 0.142 Angle : 0.546 10.502 10928 Z= 0.288 Chirality : 0.042 0.147 1299 Planarity : 0.004 0.065 1387 Dihedral : 4.407 38.074 1206 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 4.60 % Allowed : 27.34 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.26), residues: 1074 helix: 2.51 (0.27), residues: 366 sheet: 0.32 (0.31), residues: 270 loop : -1.44 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.012 0.001 TYR E 50 PHE 0.018 0.002 PHE C 199 TRP 0.018 0.002 TRP C 211 HIS 0.007 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7988) covalent geometry : angle 0.54333 (10924) SS BOND : bond 0.00225 ( 2) SS BOND : angle 3.08351 ( 4) hydrogen bonds : bond 0.03673 ( 428) hydrogen bonds : angle 4.28461 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.88 seconds wall clock time: 37 minutes 20.44 seconds (2240.44 seconds total)