Starting phenix.real_space_refine on Wed Feb 12 19:58:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxt_36712/02_2025/8jxt_36712_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxt_36712/02_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_36712/02_2025/8jxt_36712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxt_36712/02_2025/8jxt_36712.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxt_36712/02_2025/8jxt_36712_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxt_36712/02_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-5592/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: 5.11, per 1000 atoms: 0.62 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: 2.19 Conformation dependent library (CDL) restraints added in 1.0 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: 2.28 Time building geometry restraints manager: 2.51 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: 1.390 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.140 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.930 ------------------------------------------------------------------------------- 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 8487 Z= 0.301 Angle : 0.685 9.267 11574 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 *********************** 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 : 0.928 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: 0.2226 time to fit residues: 45.0292 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 : 0.939 ------------------------------------------------------------------------------- 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: 0.3677 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 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 8487 Z= 0.164 Angle : 0.548 6.713 11574 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 *********************** 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 : 0.905 Fit side-chains REVERT: C 280 LYS cc_start: 0.7829 (tttm) cc_final: 0.7570 (tttm) REVERT: R 144 PHE cc_start: 0.8086 (t80) cc_final: 0.7805 (t80) outliers start: 4 outliers final: 4 residues processed: 114 average time/residue: 0.2161 time to fit residues: 33.7495 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 : 0.873 ------------------------------------------------------------------------------- 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: 0.5980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.198943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.152583 restraints weight = 9166.205| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 3.83 r_work: 0.3576 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8487 Z= 0.229 Angle : 0.576 7.880 11574 Z= 0.308 Chirality : 0.044 0.148 1353 Planarity : 0.005 0.057 1454 Dihedral : 4.324 18.708 1178 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % 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: -0.08 (0.26), residues: 1089 helix: 1.46 (0.28), residues: 372 sheet: 0.27 (0.31), residues: 288 loop : -1.66 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 332 HIS 0.005 0.001 HIS E 35 PHE 0.017 0.002 PHE C 199 TYR 0.020 0.002 TYR E 50 ARG 0.004 0.000 ARG C 314 *********************** 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 119 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.928 Fit side-chains REVERT: B 346 ASN cc_start: 0.7204 (m110) cc_final: 0.6846 (m-40) REVERT: C 280 LYS cc_start: 0.7997 (tttm) cc_final: 0.7792 (tttm) REVERT: C 301 LYS cc_start: 0.8099 (mttp) cc_final: 0.7655 (mmtm) REVERT: R 144 PHE cc_start: 0.8196 (t80) cc_final: 0.7891 (t80) outliers start: 12 outliers final: 9 residues processed: 113 average time/residue: 0.2134 time to fit residues: 33.5316 Evaluate side-chains 105 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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: 0.0570 chunk 22 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 0.0170 chunk 27 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.4340 r_free = 0.4340 target = 0.200203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.155735 restraints weight = 9034.740| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 3.17 r_work: 0.3599 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8487 Z= 0.165 Angle : 0.516 6.480 11574 Z= 0.276 Chirality : 0.042 0.144 1353 Planarity : 0.004 0.054 1454 Dihedral : 4.128 18.594 1178 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.18 % Allowed : 11.22 % Favored : 87.60 % 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: 1.68 (0.29), residues: 372 sheet: 0.45 (0.32), residues: 282 loop : -1.57 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 332 HIS 0.003 0.001 HIS E 233 PHE 0.014 0.001 PHE B 189 TYR 0.014 0.001 TYR E 50 ARG 0.006 0.000 ARG C 314 *********************** 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: 10 poor density : 107 time to evaluate : 0.886 Fit side-chains REVERT: B 33 GLU cc_start: 0.8055 (pt0) cc_final: 0.7785 (pt0) REVERT: B 198 MET cc_start: 0.7686 (mtp) cc_final: 0.7420 (ttm) REVERT: B 346 ASN cc_start: 0.7126 (m110) cc_final: 0.6821 (m-40) REVERT: C 280 LYS cc_start: 0.7976 (tttm) cc_final: 0.7660 (tttm) REVERT: C 301 LYS cc_start: 0.8093 (mttp) cc_final: 0.7691 (mmtm) REVERT: R 144 PHE cc_start: 0.8256 (t80) cc_final: 0.7975 (t80) outliers start: 10 outliers final: 9 residues processed: 111 average time/residue: 0.2114 time to fit residues: 32.0811 Evaluate side-chains 107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 E residue 6 GLU Chi-restraints excluded: chain E residue 7 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 88 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 70 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 E 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.203131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.157021 restraints weight = 8967.803| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 3.35 r_work: 0.3651 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8487 Z= 0.129 Angle : 0.487 6.281 11574 Z= 0.257 Chirality : 0.041 0.144 1353 Planarity : 0.004 0.052 1454 Dihedral : 3.920 19.165 1178 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.30 % Allowed : 12.40 % Favored : 86.30 % 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: 0.31 (0.26), residues: 1089 helix: 1.88 (0.29), residues: 373 sheet: 0.36 (0.32), residues: 279 loop : -1.41 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 332 HIS 0.002 0.001 HIS E 233 PHE 0.014 0.001 PHE B 189 TYR 0.010 0.001 TYR E 102 ARG 0.005 0.000 ARG C 304 *********************** 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 119 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.905 Fit side-chains REVERT: B 33 GLU cc_start: 0.7855 (pt0) cc_final: 0.7630 (pt0) REVERT: B 346 ASN cc_start: 0.7040 (m110) cc_final: 0.6728 (m-40) REVERT: C 280 LYS cc_start: 0.7875 (tttm) cc_final: 0.7432 (tttm) REVERT: C 301 LYS cc_start: 0.8054 (mttp) cc_final: 0.7718 (mmtm) REVERT: C 332 TRP cc_start: 0.7757 (m-10) cc_final: 0.7493 (m-10) REVERT: E 205 SER cc_start: 0.6916 (t) cc_final: 0.6643 (m) REVERT: R 144 PHE cc_start: 0.8148 (t80) cc_final: 0.7898 (t80) REVERT: R 195 MET cc_start: 0.6319 (mmp) cc_final: 0.5122 (ttm) outliers start: 11 outliers final: 9 residues processed: 115 average time/residue: 0.2101 time to fit residues: 33.1061 Evaluate side-chains 110 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 3.9990 chunk 83 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 0.0470 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.198926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.152246 restraints weight = 9096.889| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 3.79 r_work: 0.3592 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8487 Z= 0.187 Angle : 0.517 6.992 11574 Z= 0.275 Chirality : 0.042 0.138 1353 Planarity : 0.004 0.053 1454 Dihedral : 4.023 17.568 1178 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.01 % Allowed : 12.75 % Favored : 85.24 % 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: 1.83 (0.29), residues: 373 sheet: 0.45 (0.32), residues: 281 loop : -1.39 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 332 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.001 PHE C 199 TYR 0.016 0.001 TYR E 50 ARG 0.005 0.000 ARG C 304 *********************** 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: 17 poor density : 107 time to evaluate : 0.921 Fit side-chains REVERT: B 53 MET cc_start: 0.6611 (mtp) cc_final: 0.6371 (mtm) REVERT: B 346 ASN cc_start: 0.7113 (m110) cc_final: 0.6789 (m-40) REVERT: C 280 LYS cc_start: 0.7946 (tttm) cc_final: 0.7518 (tttm) REVERT: C 301 LYS cc_start: 0.7954 (mttp) cc_final: 0.7544 (mmtm) REVERT: C 332 TRP cc_start: 0.7768 (m-10) cc_final: 0.7509 (m-10) REVERT: R 144 PHE cc_start: 0.8136 (t80) cc_final: 0.7881 (t80) outliers start: 17 outliers final: 14 residues processed: 115 average time/residue: 0.2182 time to fit residues: 34.6348 Evaluate side-chains 114 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 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 215 LEU Chi-restraints excluded: chain R residue 42 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: 0.9980 chunk 53 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.0000 chunk 46 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4342 r_free = 0.4342 target = 0.199589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.153018 restraints weight = 9068.607| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 3.53 r_work: 0.3600 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8487 Z= 0.176 Angle : 0.515 6.816 11574 Z= 0.275 Chirality : 0.042 0.136 1353 Planarity : 0.004 0.053 1454 Dihedral : 4.034 20.547 1178 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: 0.34 (0.26), residues: 1089 helix: 1.82 (0.28), residues: 373 sheet: 0.47 (0.32), residues: 281 loop : -1.39 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 332 HIS 0.004 0.001 HIS E 35 PHE 0.028 0.001 PHE R 180 TYR 0.014 0.001 TYR E 50 ARG 0.005 0.000 ARG C 304 *********************** 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 124 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.893 Fit side-chains REVERT: B 33 GLU cc_start: 0.8054 (pt0) cc_final: 0.7756 (pt0) REVERT: B 346 ASN cc_start: 0.7223 (m110) cc_final: 0.6923 (m-40) REVERT: C 280 LYS cc_start: 0.7978 (tttm) cc_final: 0.7508 (tttm) REVERT: C 301 LYS cc_start: 0.7958 (mttp) cc_final: 0.7562 (mmtm) REVERT: C 332 TRP cc_start: 0.7830 (m-10) cc_final: 0.7488 (m-10) REVERT: R 144 PHE cc_start: 0.8181 (t80) cc_final: 0.7921 (t80) outliers start: 18 outliers final: 12 residues processed: 115 average time/residue: 0.2095 time to fit residues: 33.4194 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 : 0.894 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 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 C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.195572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.149852 restraints weight = 9133.150| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 3.66 r_work: 0.3546 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8487 Z= 0.269 Angle : 0.595 8.707 11574 Z= 0.315 Chirality : 0.044 0.164 1353 Planarity : 0.004 0.054 1454 Dihedral : 4.375 30.864 1178 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.89 % Allowed : 13.70 % Favored : 84.42 % 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: 0.14 (0.26), residues: 1089 helix: 1.63 (0.28), residues: 375 sheet: 0.38 (0.32), residues: 281 loop : -1.51 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 332 HIS 0.007 0.001 HIS E 233 PHE 0.027 0.002 PHE R 180 TYR 0.023 0.002 TYR E 50 ARG 0.005 0.001 ARG C 304 *********************** 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: 16 poor density : 102 time to evaluate : 0.869 Fit side-chains REVERT: B 346 ASN cc_start: 0.7329 (m110) cc_final: 0.7042 (m-40) REVERT: C 76 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6803 (m-30) REVERT: C 280 LYS cc_start: 0.8097 (tttm) cc_final: 0.7663 (tttm) REVERT: C 332 TRP cc_start: 0.7875 (m-10) cc_final: 0.7544 (m-10) outliers start: 16 outliers final: 13 residues processed: 109 average time/residue: 0.1991 time to fit residues: 30.3031 Evaluate side-chains 111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 215 LEU Chi-restraints excluded: chain R residue 42 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.197069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.150515 restraints weight = 9193.487| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.78 r_work: 0.3564 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8487 Z= 0.219 Angle : 0.556 8.091 11574 Z= 0.295 Chirality : 0.043 0.150 1353 Planarity : 0.004 0.053 1454 Dihedral : 4.328 37.520 1178 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.77 % Allowed : 14.29 % Favored : 83.94 % 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: 0.27 (0.26), residues: 1089 helix: 1.78 (0.28), residues: 371 sheet: 0.39 (0.32), residues: 281 loop : -1.39 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 332 HIS 0.005 0.001 HIS E 233 PHE 0.028 0.001 PHE R 180 TYR 0.018 0.002 TYR E 50 ARG 0.005 0.000 ARG C 304 *********************** 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 113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.841 Fit side-chains REVERT: B 33 GLU cc_start: 0.8244 (pt0) cc_final: 0.7935 (pt0) REVERT: B 346 ASN cc_start: 0.7271 (m110) cc_final: 0.7034 (m-40) REVERT: C 76 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6861 (m-30) REVERT: C 268 ASN cc_start: 0.8046 (m110) cc_final: 0.7338 (t0) REVERT: C 280 LYS cc_start: 0.8057 (tttm) cc_final: 0.7571 (tttm) REVERT: C 332 TRP cc_start: 0.7797 (m-10) cc_final: 0.7460 (m-10) outliers start: 15 outliers final: 14 residues processed: 105 average time/residue: 0.2048 time to fit residues: 30.2325 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 : 0.970 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.198672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.152922 restraints weight = 9012.643| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.74 r_work: 0.3605 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8487 Z= 0.160 Angle : 0.524 8.891 11574 Z= 0.275 Chirality : 0.041 0.140 1353 Planarity : 0.004 0.052 1454 Dihedral : 4.170 41.272 1178 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.06 % Allowed : 14.99 % Favored : 83.94 % 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: 0.46 (0.26), residues: 1089 helix: 2.09 (0.29), residues: 361 sheet: 0.46 (0.32), residues: 281 loop : -1.35 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 332 HIS 0.003 0.001 HIS E 233 PHE 0.028 0.001 PHE R 180 TYR 0.014 0.001 TYR E 191 ARG 0.005 0.000 ARG C 304 ********************** 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 109 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.962 Fit side-chains REVERT: B 33 GLU cc_start: 0.8140 (pt0) cc_final: 0.7833 (pt0) REVERT: B 346 ASN cc_start: 0.7141 (m110) cc_final: 0.6852 (m-40) REVERT: C 268 ASN cc_start: 0.8029 (m110) cc_final: 0.7379 (t0) REVERT: C 280 LYS cc_start: 0.7874 (tttm) cc_final: 0.7430 (tttm) REVERT: C 301 LYS cc_start: 0.8027 (mttp) cc_final: 0.7590 (mmtm) REVERT: C 332 TRP cc_start: 0.7734 (m-10) cc_final: 0.7431 (m-10) outliers start: 9 outliers final: 9 residues processed: 106 average time/residue: 0.2037 time to fit residues: 29.9370 Evaluate side-chains 107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL 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 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: 2.9990 chunk 89 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.195379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.150123 restraints weight = 9179.569| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 3.49 r_work: 0.3553 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8487 Z= 0.244 Angle : 0.577 8.839 11574 Z= 0.305 Chirality : 0.043 0.150 1353 Planarity : 0.004 0.054 1454 Dihedral : 4.418 50.447 1178 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.53 % Allowed : 14.40 % Favored : 84.06 % 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: 1.88 (0.28), residues: 367 sheet: 0.39 (0.32), residues: 281 loop : -1.37 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 332 HIS 0.006 0.001 HIS E 233 PHE 0.027 0.002 PHE R 180 TYR 0.020 0.002 TYR E 50 ARG 0.005 0.000 ARG C 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4665.89 seconds wall clock time: 83 minutes 18.09 seconds (4998.09 seconds total)