Starting phenix.real_space_refine on Tue Apr 29 02:45:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxt_36712/04_2025/8jxt_36712_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxt_36712/04_2025/8jxt_36712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxt_36712/04_2025/8jxt_36712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxt_36712/04_2025/8jxt_36712.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxt_36712/04_2025/8jxt_36712_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxt_36712/04_2025/8jxt_36712_neut.cif" } resolution = 3.07 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= -0.003 sd= 0.121 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 54 5.16 5 C 5330 2.51 5 N 1365 2.21 5 O 1548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8298 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1627 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2489 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 336 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1728 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2105 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {'HSM': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.03, per 1000 atoms: 0.61 Number of scatterers: 8298 At special positions: 0 Unit cell: (91.3, 124.3, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 1 15.00 O 1548 8.00 N 1365 7.00 C 5330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.04 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " 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: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 36.7% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'B' and resid 6 through 30 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.586A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.673A pdb=" N CYS B 214 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.808A pdb=" N GLU B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.912A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.789A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 26 Processing helix chain 'C' and resid 29 through 37 removed outlier: 4.363A pdb=" N THR C 34 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASN C 35 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN C 36 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 24 removed outlier: 3.672A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.672A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 removed outlier: 4.359A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 43 removed outlier: 4.064A pdb=" N VAL R 36 " --> pdb=" O GLY R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 78 removed outlier: 3.805A pdb=" N GLY R 65 " --> pdb=" O ASP R 61 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL R 66 " --> pdb=" O PHE R 62 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER R 68 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix Proline residue: R 74 - end of helix removed outlier: 3.571A pdb=" N PHE R 78 " --> pdb=" O PRO R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 118 removed outlier: 4.199A pdb=" N PHE R 89 " --> pdb=" O GLU R 85 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 124 Processing helix chain 'R' and resid 130 through 153 removed outlier: 3.977A pdb=" N TRP R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 171 through 181 removed outlier: 3.899A pdb=" N LEU R 175 " --> pdb=" O GLU R 171 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE R 177 " --> pdb=" O TYR R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 203 removed outlier: 4.016A pdb=" N LYS R 203 " --> pdb=" O TRP R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 329 removed outlier: 4.435A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 4.466A pdb=" N TYR R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 349 removed outlier: 3.904A pdb=" N TRP R 345 " --> pdb=" O ARG R 341 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN R 347 " --> pdb=" O ALA R 343 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE R 349 " --> pdb=" O TRP R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 362 removed outlier: 3.584A pdb=" N VAL R 353 " --> pdb=" O PHE R 349 " (cutoff:3.500A) Proline residue: R 355 - end of helix removed outlier: 3.548A pdb=" N TYR R 358 " --> pdb=" O ASN R 354 " (cutoff:3.500A) Proline residue: R 359 - end of helix removed outlier: 4.162A pdb=" N HIS R 362 " --> pdb=" O TYR R 358 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 371 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.923A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ALA B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.054A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.070A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.042A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 7.109A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.069A 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: 6.747A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.169A 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: 6.745A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.566A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.157A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.264A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 142 through 143 removed outlier: 3.567A pdb=" N THR E 142 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 161 " --> pdb=" O THR E 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.554A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1116 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: 2.31 Time building geometry restraints manager: 2.28 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: 2636 1.34 - 1.46: 2224 1.46 - 1.59: 3550 1.59 - 1.71: 0 1.71 - 1.83: 77 Bond restraints: 8487 Sorted by residual: bond pdb=" O3 PO4 R 402 " pdb=" P PO4 R 402 " ideal model delta sigma weight residual 1.569 1.524 0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" CB HSM R 401 " pdb=" CG HSM R 401 " ideal model delta sigma weight residual 1.496 1.452 0.044 2.00e-02 2.50e+03 4.88e+00 bond pdb=" O2 PO4 R 402 " pdb=" P PO4 R 402 " ideal model delta sigma weight residual 1.567 1.523 0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" O4 PO4 R 402 " pdb=" P PO4 R 402 " ideal model delta sigma weight residual 1.568 1.525 0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" O1 PO4 R 402 " pdb=" P PO4 R 402 " ideal model delta sigma weight residual 1.565 1.524 0.041 2.00e-02 2.50e+03 4.27e+00 ... (remaining 8482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 11302 1.85 - 3.71: 225 3.71 - 5.56: 37 5.56 - 7.41: 8 7.41 - 9.27: 2 Bond angle restraints: 11574 Sorted by residual: angle pdb=" CA MET E 193 " pdb=" CB MET E 193 " pdb=" CG MET E 193 " ideal model delta sigma weight residual 114.10 120.62 -6.52 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA TRP C 82 " pdb=" CB TRP C 82 " pdb=" CG TRP C 82 " ideal model delta sigma weight residual 113.60 119.78 -6.18 1.90e+00 2.77e-01 1.06e+01 angle pdb=" CA HSM R 401 " pdb=" CB HSM R 401 " pdb=" CG HSM R 401 " ideal model delta sigma weight residual 114.47 105.20 9.27 3.00e+00 1.11e-01 9.54e+00 angle pdb=" N MET E 193 " pdb=" CA MET E 193 " pdb=" CB MET E 193 " ideal model delta sigma weight residual 114.27 109.28 4.99 1.64e+00 3.72e-01 9.26e+00 angle pdb=" CG MET E 193 " pdb=" SD MET E 193 " pdb=" CE MET E 193 " ideal model delta sigma weight residual 100.90 107.53 -6.63 2.20e+00 2.07e-01 9.09e+00 ... (remaining 11569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4515 17.57 - 35.14: 334 35.14 - 52.70: 49 52.70 - 70.27: 7 70.27 - 87.84: 1 Dihedral angle restraints: 4906 sinusoidal: 1690 harmonic: 3216 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 136.07 -43.07 1 1.00e+01 1.00e-02 2.59e+01 dihedral pdb=" CA ARG E 192 " pdb=" C ARG E 192 " pdb=" N MET E 193 " pdb=" CA MET E 193 " ideal model delta harmonic sigma weight residual 180.00 155.69 24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA TRP C 339 " pdb=" C TRP C 339 " pdb=" N ASN C 340 " pdb=" CA ASN C 340 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 4903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 735 0.030 - 0.059: 392 0.059 - 0.089: 145 0.089 - 0.119: 65 0.119 - 0.148: 16 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA PRO R 318 " pdb=" N PRO R 318 " pdb=" C PRO R 318 " pdb=" CB PRO R 318 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE C 58 " pdb=" N ILE C 58 " pdb=" C ILE C 58 " pdb=" CB ILE C 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE C 229 " pdb=" N ILE C 229 " pdb=" C ILE C 229 " pdb=" CB ILE C 229 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1350 not shown) Planarity restraints: 1454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU R 165 " 0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO R 166 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO R 166 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 166 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.45e+00 pdb=" N PRO C 236 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.036 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=" C ASP D 48 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.71e+00 pdb=" N PRO D 49 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " 0.030 5.00e-02 4.00e+02 ... (remaining 1451 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1403 2.76 - 3.30: 7407 3.30 - 3.83: 12744 3.83 - 4.37: 13796 4.37 - 4.90: 25240 Nonbonded interactions: 60590 Sorted by model distance: nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.228 3.040 nonbonded pdb=" O GLY E 210 " pdb=" OG1 THR E 211 " model vdw 2.264 3.040 nonbonded pdb=" OD1 ASP C 290 " pdb=" NE ARG C 314 " model vdw 2.284 3.120 nonbonded pdb=" NH2 ARG E 203 " pdb=" OE2 GLU E 221 " model vdw 2.288 3.120 nonbonded pdb=" NH1 ARG E 38 " pdb=" OD1 ASP E 90 " model vdw 2.298 3.120 ... (remaining 60585 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: 1.180 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.350 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 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 : 0.005 0.045 8489 Z= 0.212 Angle : 0.685 9.267 11578 Z= 0.388 Chirality : 0.045 0.148 1353 Planarity : 0.005 0.088 1454 Dihedral : 12.498 87.839 2824 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.33 (0.26), residues: 1089 helix: 1.28 (0.28), residues: 357 sheet: 0.34 (0.32), residues: 274 loop : -1.83 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 82 HIS 0.007 0.002 HIS R 75 PHE 0.027 0.002 PHE C 199 TYR 0.017 0.002 TYR E 50 ARG 0.012 0.001 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.13336 ( 396) hydrogen bonds : angle 5.14314 ( 1116) SS BOND : bond 0.00897 ( 2) SS BOND : angle 0.83415 ( 4) covalent geometry : bond 0.00460 ( 8487) covalent geometry : angle 0.68473 (11574) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: C 262 MET cc_start: 0.7771 (mmt) cc_final: 0.7513 (mpp) REVERT: E 205 SER cc_start: 0.7476 (t) cc_final: 0.7198 (m) outliers start: 2 outliers final: 0 residues processed: 150 average time/residue: 0.2130 time to fit residues: 43.4388 Evaluate side-chains 109 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 0.0050 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 44 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 268 ASN E 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.203687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.158585 restraints weight = 8987.730| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 3.49 r_work: 0.3676 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8489 Z= 0.122 Angle : 0.548 6.713 11578 Z= 0.293 Chirality : 0.042 0.142 1353 Planarity : 0.004 0.063 1454 Dihedral : 4.285 17.466 1178 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.47 % Allowed : 6.85 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.07 (0.26), residues: 1089 helix: 1.46 (0.28), residues: 370 sheet: 0.29 (0.31), residues: 284 loop : -1.64 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 82 HIS 0.003 0.001 HIS B 188 PHE 0.019 0.001 PHE R 144 TYR 0.012 0.001 TYR E 50 ARG 0.003 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.05416 ( 396) hydrogen bonds : angle 4.43364 ( 1116) SS BOND : bond 0.00842 ( 2) SS BOND : angle 1.01526 ( 4) covalent geometry : bond 0.00248 ( 8487) covalent geometry : angle 0.54780 (11574) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.811 Fit side-chains REVERT: C 280 LYS cc_start: 0.7839 (tttm) cc_final: 0.7574 (tttm) REVERT: R 144 PHE cc_start: 0.8088 (t80) cc_final: 0.7806 (t80) outliers start: 4 outliers final: 4 residues processed: 114 average time/residue: 0.2081 time to fit residues: 32.6425 Evaluate side-chains 101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN E 184 GLN R 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.197174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150268 restraints weight = 9172.327| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 4.08 r_work: 0.3554 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8489 Z= 0.180 Angle : 0.605 8.713 11578 Z= 0.324 Chirality : 0.045 0.153 1353 Planarity : 0.005 0.058 1454 Dihedral : 4.444 18.612 1178 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.42 % Allowed : 9.33 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.15 (0.26), residues: 1089 helix: 1.37 (0.28), residues: 372 sheet: 0.19 (0.31), residues: 292 loop : -1.66 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 332 HIS 0.006 0.001 HIS E 35 PHE 0.019 0.002 PHE C 199 TYR 0.023 0.002 TYR E 50 ARG 0.003 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.06293 ( 396) hydrogen bonds : angle 4.43841 ( 1116) SS BOND : bond 0.00725 ( 2) SS BOND : angle 0.80205 ( 4) covalent geometry : bond 0.00418 ( 8487) covalent geometry : angle 0.60514 (11574) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.829 Fit side-chains REVERT: B 33 GLU cc_start: 0.8256 (pt0) cc_final: 0.8019 (pt0) REVERT: B 346 ASN cc_start: 0.7216 (m110) cc_final: 0.6844 (m-40) REVERT: C 204 CYS cc_start: 0.7796 (t) cc_final: 0.7538 (t) REVERT: C 280 LYS cc_start: 0.8050 (tttm) cc_final: 0.7828 (tttm) REVERT: C 301 LYS cc_start: 0.8098 (mttp) cc_final: 0.7624 (mmtm) outliers start: 12 outliers final: 9 residues processed: 115 average time/residue: 0.1941 time to fit residues: 31.0107 Evaluate side-chains 104 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 8 optimal weight: 0.0070 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 64 optimal weight: 0.0470 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.9498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 110 ASN E 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.197985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.151063 restraints weight = 9069.676| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.91 r_work: 0.3571 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8489 Z= 0.136 Angle : 0.544 7.482 11578 Z= 0.292 Chirality : 0.042 0.145 1353 Planarity : 0.004 0.055 1454 Dihedral : 4.281 18.829 1178 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.77 % Allowed : 11.10 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.02 (0.26), residues: 1089 helix: 1.53 (0.28), residues: 373 sheet: 0.35 (0.31), residues: 285 loop : -1.61 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 332 HIS 0.004 0.001 HIS E 233 PHE 0.014 0.001 PHE B 189 TYR 0.017 0.001 TYR E 50 ARG 0.003 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.05388 ( 396) hydrogen bonds : angle 4.26169 ( 1116) SS BOND : bond 0.00464 ( 2) SS BOND : angle 1.00143 ( 4) covalent geometry : bond 0.00302 ( 8487) covalent geometry : angle 0.54329 (11574) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.894 Fit side-chains REVERT: B 346 ASN cc_start: 0.7150 (m110) cc_final: 0.6848 (m-40) REVERT: C 76 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6819 (m-30) REVERT: C 280 LYS cc_start: 0.8048 (tttm) cc_final: 0.7727 (tttm) REVERT: C 301 LYS cc_start: 0.7949 (mttp) cc_final: 0.7488 (mmtm) REVERT: E 67 ARG cc_start: 0.6379 (ttt-90) cc_final: 0.5956 (ttp80) REVERT: R 144 PHE cc_start: 0.8038 (t80) cc_final: 0.7756 (t80) outliers start: 15 outliers final: 11 residues processed: 110 average time/residue: 0.1989 time to fit residues: 30.5364 Evaluate side-chains 111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 8 optimal weight: 0.0670 chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 0.0570 chunk 25 optimal weight: 2.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN E 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.200972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.154296 restraints weight = 8978.015| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.65 r_work: 0.3615 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8489 Z= 0.108 Angle : 0.500 7.238 11578 Z= 0.267 Chirality : 0.041 0.145 1353 Planarity : 0.004 0.053 1454 Dihedral : 4.077 19.736 1178 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.01 % Allowed : 12.51 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.26), residues: 1089 helix: 1.75 (0.29), residues: 373 sheet: 0.43 (0.32), residues: 276 loop : -1.45 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 332 HIS 0.004 0.001 HIS B 188 PHE 0.014 0.001 PHE B 189 TYR 0.012 0.001 TYR E 50 ARG 0.003 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 396) hydrogen bonds : angle 4.05155 ( 1116) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.71876 ( 4) covalent geometry : bond 0.00220 ( 8487) covalent geometry : angle 0.50034 (11574) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: B 33 GLU cc_start: 0.7983 (pt0) cc_final: 0.7663 (pt0) REVERT: B 346 ASN cc_start: 0.7066 (m110) cc_final: 0.6750 (m-40) REVERT: C 280 LYS cc_start: 0.7935 (tttm) cc_final: 0.7519 (tttm) REVERT: C 301 LYS cc_start: 0.7933 (mttp) cc_final: 0.7530 (mmtm) REVERT: E 67 ARG cc_start: 0.6439 (ttt-90) cc_final: 0.6170 (ttp80) REVERT: R 144 PHE cc_start: 0.8177 (t80) cc_final: 0.7909 (t80) outliers start: 17 outliers final: 10 residues processed: 115 average time/residue: 0.2068 time to fit residues: 32.4825 Evaluate side-chains 107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 349 PHE Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 0.0060 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 HIS B 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.198129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.151187 restraints weight = 9130.868| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 4.07 r_work: 0.3573 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8489 Z= 0.136 Angle : 0.541 7.687 11578 Z= 0.287 Chirality : 0.042 0.136 1353 Planarity : 0.004 0.054 1454 Dihedral : 4.180 21.313 1178 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.13 % Allowed : 12.87 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.16 (0.26), residues: 1089 helix: 1.65 (0.28), residues: 373 sheet: 0.37 (0.32), residues: 281 loop : -1.47 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 332 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.001 PHE C 199 TYR 0.017 0.001 TYR E 50 ARG 0.011 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.05234 ( 396) hydrogen bonds : angle 4.11843 ( 1116) SS BOND : bond 0.00440 ( 2) SS BOND : angle 0.78816 ( 4) covalent geometry : bond 0.00308 ( 8487) covalent geometry : angle 0.54063 (11574) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: B 346 ASN cc_start: 0.7177 (m110) cc_final: 0.6878 (m-40) REVERT: C 280 LYS cc_start: 0.7998 (tttm) cc_final: 0.7561 (tttm) REVERT: C 301 LYS cc_start: 0.8003 (mttp) cc_final: 0.7631 (mmtm) REVERT: C 332 TRP cc_start: 0.7754 (m-10) cc_final: 0.7417 (m-10) REVERT: R 144 PHE cc_start: 0.8170 (t80) cc_final: 0.7896 (t80) outliers start: 18 outliers final: 16 residues processed: 114 average time/residue: 0.2064 time to fit residues: 32.6074 Evaluate side-chains 116 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 349 PHE Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.199056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.152641 restraints weight = 9061.842| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 3.51 r_work: 0.3591 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8489 Z= 0.124 Angle : 0.533 7.046 11578 Z= 0.281 Chirality : 0.042 0.138 1353 Planarity : 0.004 0.053 1454 Dihedral : 4.133 24.214 1178 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.13 % Allowed : 13.34 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.23 (0.26), residues: 1089 helix: 1.74 (0.28), residues: 373 sheet: 0.42 (0.32), residues: 281 loop : -1.47 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 332 HIS 0.004 0.001 HIS C 225 PHE 0.013 0.001 PHE B 189 TYR 0.015 0.001 TYR E 50 ARG 0.005 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 396) hydrogen bonds : angle 4.05895 ( 1116) SS BOND : bond 0.00393 ( 2) SS BOND : angle 0.71084 ( 4) covalent geometry : bond 0.00276 ( 8487) covalent geometry : angle 0.53272 (11574) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.813 Fit side-chains REVERT: B 33 GLU cc_start: 0.8061 (pt0) cc_final: 0.7769 (pt0) REVERT: B 346 ASN cc_start: 0.7249 (m110) cc_final: 0.6947 (m-40) REVERT: C 76 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6819 (m-30) REVERT: C 280 LYS cc_start: 0.7947 (tttm) cc_final: 0.7506 (tttm) REVERT: C 301 LYS cc_start: 0.8010 (mttp) cc_final: 0.7671 (mmtm) REVERT: C 332 TRP cc_start: 0.7777 (m-10) cc_final: 0.7449 (m-10) REVERT: R 144 PHE cc_start: 0.8141 (t80) cc_final: 0.7877 (t80) outliers start: 18 outliers final: 13 residues processed: 111 average time/residue: 0.2025 time to fit residues: 30.9504 Evaluate side-chains 112 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.196346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.149483 restraints weight = 9133.569| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.85 r_work: 0.3554 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8489 Z= 0.159 Angle : 0.573 8.313 11578 Z= 0.304 Chirality : 0.043 0.157 1353 Planarity : 0.004 0.054 1454 Dihedral : 4.340 31.078 1178 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.24 % Allowed : 13.46 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.11 (0.26), residues: 1089 helix: 1.60 (0.28), residues: 375 sheet: 0.38 (0.32), residues: 281 loop : -1.55 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 332 HIS 0.005 0.001 HIS E 233 PHE 0.015 0.001 PHE C 199 TYR 0.020 0.002 TYR E 50 ARG 0.004 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.05674 ( 396) hydrogen bonds : angle 4.21002 ( 1116) SS BOND : bond 0.00492 ( 2) SS BOND : angle 0.83234 ( 4) covalent geometry : bond 0.00371 ( 8487) covalent geometry : angle 0.57275 (11574) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.934 Fit side-chains REVERT: B 346 ASN cc_start: 0.7352 (m110) cc_final: 0.7070 (m-40) REVERT: C 76 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6804 (m-30) REVERT: C 280 LYS cc_start: 0.8091 (tttm) cc_final: 0.7675 (tttm) REVERT: C 332 TRP cc_start: 0.7904 (m-10) cc_final: 0.7632 (m-10) outliers start: 19 outliers final: 14 residues processed: 110 average time/residue: 0.2071 time to fit residues: 31.9673 Evaluate side-chains 111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.197865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.152537 restraints weight = 9100.471| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.67 r_work: 0.3595 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8489 Z= 0.119 Angle : 0.526 7.330 11578 Z= 0.281 Chirality : 0.042 0.141 1353 Planarity : 0.004 0.053 1454 Dihedral : 4.205 34.653 1178 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.13 % Allowed : 14.05 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.33 (0.26), residues: 1089 helix: 1.89 (0.29), residues: 367 sheet: 0.43 (0.32), residues: 281 loop : -1.41 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 332 HIS 0.004 0.001 HIS E 35 PHE 0.032 0.001 PHE R 180 TYR 0.014 0.001 TYR E 50 ARG 0.004 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.04882 ( 396) hydrogen bonds : angle 4.07197 ( 1116) SS BOND : bond 0.00374 ( 2) SS BOND : angle 0.67610 ( 4) covalent geometry : bond 0.00260 ( 8487) covalent geometry : angle 0.52589 (11574) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.859 Fit side-chains REVERT: B 33 GLU cc_start: 0.8146 (pt0) cc_final: 0.7828 (pt0) REVERT: B 346 ASN cc_start: 0.7183 (m110) cc_final: 0.6897 (m-40) REVERT: C 76 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6841 (m-30) REVERT: C 268 ASN cc_start: 0.7973 (m110) cc_final: 0.7289 (t0) REVERT: C 280 LYS cc_start: 0.7906 (tttm) cc_final: 0.7429 (tttm) REVERT: C 332 TRP cc_start: 0.7678 (m-10) cc_final: 0.7380 (m-10) REVERT: R 144 PHE cc_start: 0.8147 (t80) cc_final: 0.7936 (t80) outliers start: 18 outliers final: 16 residues processed: 108 average time/residue: 0.2645 time to fit residues: 40.4729 Evaluate side-chains 111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 93 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.197450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.150718 restraints weight = 9030.930| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.81 r_work: 0.3581 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8489 Z= 0.124 Angle : 0.533 7.508 11578 Z= 0.283 Chirality : 0.042 0.138 1353 Planarity : 0.004 0.053 1454 Dihedral : 4.215 39.242 1178 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.01 % Allowed : 14.17 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.34 (0.26), residues: 1089 helix: 1.90 (0.28), residues: 368 sheet: 0.44 (0.32), residues: 281 loop : -1.41 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 332 HIS 0.004 0.001 HIS E 35 PHE 0.030 0.001 PHE R 180 TYR 0.015 0.001 TYR E 50 ARG 0.004 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 396) hydrogen bonds : angle 4.04824 ( 1116) SS BOND : bond 0.00408 ( 2) SS BOND : angle 0.64554 ( 4) covalent geometry : bond 0.00278 ( 8487) covalent geometry : angle 0.53249 (11574) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.869 Fit side-chains REVERT: B 33 GLU cc_start: 0.8212 (pt0) cc_final: 0.7885 (pt0) REVERT: B 346 ASN cc_start: 0.7189 (m110) cc_final: 0.6904 (m-40) REVERT: C 268 ASN cc_start: 0.7984 (m110) cc_final: 0.7316 (t0) REVERT: C 280 LYS cc_start: 0.7905 (tttm) cc_final: 0.7437 (tttm) REVERT: C 332 TRP cc_start: 0.7708 (m-10) cc_final: 0.7462 (m-10) outliers start: 17 outliers final: 16 residues processed: 108 average time/residue: 0.2818 time to fit residues: 41.2143 Evaluate side-chains 113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 360 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 75 optimal weight: 0.1980 chunk 45 optimal weight: 7.9990 chunk 12 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.199414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.153197 restraints weight = 9152.681| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.81 r_work: 0.3606 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8489 Z= 0.110 Angle : 0.517 8.350 11578 Z= 0.274 Chirality : 0.041 0.138 1353 Planarity : 0.004 0.052 1454 Dihedral : 4.152 43.457 1178 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.53 % Allowed : 14.88 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.47 (0.26), residues: 1089 helix: 2.11 (0.29), residues: 361 sheet: 0.49 (0.32), residues: 281 loop : -1.36 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 332 HIS 0.003 0.001 HIS E 35 PHE 0.034 0.001 PHE R 144 TYR 0.011 0.001 TYR E 50 ARG 0.004 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 396) hydrogen bonds : angle 3.97525 ( 1116) SS BOND : bond 0.00344 ( 2) SS BOND : angle 0.57435 ( 4) covalent geometry : bond 0.00239 ( 8487) covalent geometry : angle 0.51678 (11574) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5066.02 seconds wall clock time: 88 minutes 30.14 seconds (5310.14 seconds total)