Starting phenix.real_space_refine on Sat May 10 16:02:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unp_42412/05_2025/8unp_42412.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unp_42412/05_2025/8unp_42412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8unp_42412/05_2025/8unp_42412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unp_42412/05_2025/8unp_42412.map" model { file = "/net/cci-nas-00/data/ceres_data/8unp_42412/05_2025/8unp_42412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unp_42412/05_2025/8unp_42412.cif" } resolution = 3.3 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= -0.000 sd= 0.027 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 3 5.49 5 S 43 5.16 5 C 4225 2.51 5 N 1130 2.21 5 O 1158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6559 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 237, 1712 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 4 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 15, 'ARG:plan': 12, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 191 Conformer: "B" Number of residues, atoms: 237, 1712 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 4 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 15, 'ARG:plan': 12, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 191 bond proxies already assigned to first conformer: 1731 Chain: "B" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2357 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 144 Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 335 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2095 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 5.84, per 1000 atoms: 0.89 Number of scatterers: 6559 At special positions: 0 Unit cell: (84.1669, 133.626, 96.3147, 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 43 16.00 P 3 15.00 O 1158 8.00 N 1130 7.00 C 4225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 1.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 47.6% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.540A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 removed outlier: 4.037A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.842A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.115A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.572A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.635A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 26 removed outlier: 4.208A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.683A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.699A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.569A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 4.071A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR R 73 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 120 Processing helix chain 'R' and resid 121 through 137 Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.829A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.719A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.703A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.729A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.854A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.376A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.590A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 7.218A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.735A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.859A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.097A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.941A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.844A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.891A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.936A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1303 1.33 - 1.45: 1701 1.45 - 1.57: 3635 1.57 - 1.69: 5 1.69 - 1.81: 59 Bond restraints: 6703 Sorted by residual: bond pdb=" CA GLN A 12 " pdb=" C GLN A 12 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.41e-02 5.03e+03 2.53e+01 bond pdb=" CA ASP A 223 " pdb=" C ASP A 223 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.23e-02 6.61e+03 1.98e+01 bond pdb=" CA THR A 325 " pdb=" C THR A 325 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.24e-02 6.50e+03 1.98e+01 bond pdb=" C5 GTP A 401 " pdb=" C6 GTP A 401 " ideal model delta sigma weight residual 1.390 1.477 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C4 GTP A 401 " pdb=" C5 GTP A 401 " ideal model delta sigma weight residual 1.390 1.469 -0.079 2.00e-02 2.50e+03 1.54e+01 ... (remaining 6698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 9050 2.87 - 5.74: 110 5.74 - 8.61: 9 8.61 - 11.49: 6 11.49 - 14.36: 2 Bond angle restraints: 9177 Sorted by residual: angle pdb=" N GLN A 12 " pdb=" CA GLN A 12 " pdb=" C GLN A 12 " ideal model delta sigma weight residual 113.16 99.62 13.54 1.24e+00 6.50e-01 1.19e+02 angle pdb=" N ARG A 228 " pdb=" CA ARG A 228 " pdb=" C ARG A 228 " ideal model delta sigma weight residual 110.10 124.46 -14.36 1.49e+00 4.50e-01 9.28e+01 angle pdb=" N ILE R 58 " pdb=" CA ILE R 58 " pdb=" C ILE R 58 " ideal model delta sigma weight residual 110.62 101.44 9.18 1.02e+00 9.61e-01 8.09e+01 angle pdb=" N THR A 263 " pdb=" CA THR A 263 " pdb=" C THR A 263 " ideal model delta sigma weight residual 110.53 100.96 9.57 1.32e+00 5.74e-01 5.26e+01 angle pdb=" N ARG A 231 " pdb=" CA ARG A 231 " pdb=" C ARG A 231 " ideal model delta sigma weight residual 110.23 100.03 10.20 1.45e+00 4.76e-01 4.95e+01 ... (remaining 9172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.82: 3801 33.82 - 67.63: 48 67.63 - 101.45: 1 101.45 - 135.27: 2 135.27 - 169.08: 3 Dihedral angle restraints: 3855 sinusoidal: 1208 harmonic: 2647 Sorted by residual: dihedral pdb=" O5' GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PA GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 274.12 105.04 169.08 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 100.64 160.23 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 291.08 152.69 138.39 1 2.00e+01 2.50e-03 4.19e+01 ... (remaining 3852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 819 0.044 - 0.088: 206 0.088 - 0.132: 70 0.132 - 0.176: 7 0.176 - 0.219: 1 Chirality restraints: 1103 Sorted by residual: chirality pdb=" CA ARG A 228 " pdb=" N ARG A 228 " pdb=" C ARG A 228 " pdb=" CB ARG A 228 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA VAL R 44 " pdb=" N VAL R 44 " pdb=" C VAL R 44 " pdb=" CB VAL R 44 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE R 58 " pdb=" N ILE R 58 " pdb=" C ILE R 58 " pdb=" CB ILE R 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 1100 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO A 321 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 42 " 0.013 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C LEU R 42 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU R 42 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE R 43 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 33 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C VAL R 33 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL R 33 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL R 34 " -0.014 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 804 2.75 - 3.28: 6231 3.28 - 3.82: 10286 3.82 - 4.36: 11339 4.36 - 4.90: 20929 Nonbonded interactions: 49589 Sorted by model distance: nonbonded pdb=" OG1 THR A 55 " pdb=" O2A GTP A 401 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.233 3.040 nonbonded pdb=" N GLN A 12 " pdb=" N ARG A 13 " model vdw 2.246 2.560 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASN A 239 " pdb=" NZ LYS B 57 " model vdw 2.307 3.120 ... (remaining 49584 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=0.49 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: 2.360 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.570 Find NCS groups from input model: 0.070 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.006 0.087 6704 Z= 0.343 Angle : 0.795 14.357 9179 Z= 0.502 Chirality : 0.044 0.219 1103 Planarity : 0.004 0.081 1145 Dihedral : 13.788 169.085 2132 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.29), residues: 889 helix: 1.96 (0.27), residues: 400 sheet: 0.16 (0.40), residues: 171 loop : -1.06 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 313 HIS 0.010 0.001 HIS A 220 PHE 0.018 0.001 PHE A 222 TYR 0.019 0.001 TYR B 59 ARG 0.002 0.000 ARG R 175 Details of bonding type rmsd hydrogen bonds : bond 0.18874 ( 348) hydrogen bonds : angle 6.77609 ( 1020) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.83043 ( 2) covalent geometry : bond 0.00552 ( 6703) covalent geometry : angle 0.79534 ( 9177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.776 Fit side-chains REVERT: A 267 GLN cc_start: 0.8277 (tp-100) cc_final: 0.7739 (tp-100) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2729 time to fit residues: 34.0472 Evaluate side-chains 72 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 220 HIS A 254 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 241 HIS R 322 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097522 restraints weight = 31550.137| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.26 r_work: 0.3047 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6704 Z= 0.141 Angle : 0.516 7.219 9179 Z= 0.276 Chirality : 0.042 0.158 1103 Planarity : 0.003 0.040 1145 Dihedral : 10.629 178.694 990 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.03 % Allowed : 8.22 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 889 helix: 2.12 (0.26), residues: 410 sheet: 0.08 (0.39), residues: 180 loop : -0.94 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.006 0.001 HIS R 241 PHE 0.016 0.001 PHE R 61 TYR 0.015 0.001 TYR B 59 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.05516 ( 348) hydrogen bonds : angle 4.65605 ( 1020) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.49140 ( 2) covalent geometry : bond 0.00311 ( 6703) covalent geometry : angle 0.51558 ( 9177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.732 Fit side-chains REVERT: A 267 GLN cc_start: 0.8118 (tp-100) cc_final: 0.7659 (tp-100) REVERT: A 311 TYR cc_start: 0.8357 (m-80) cc_final: 0.8149 (m-80) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.1771 time to fit residues: 19.4349 Evaluate side-chains 76 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain R residue 143 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 74 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.097091 restraints weight = 43347.380| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 5.42 r_work: 0.2984 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6704 Z= 0.101 Angle : 0.465 7.314 9179 Z= 0.246 Chirality : 0.040 0.158 1103 Planarity : 0.003 0.038 1145 Dihedral : 10.394 179.721 990 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.68 % Allowed : 10.27 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.29), residues: 889 helix: 2.31 (0.26), residues: 410 sheet: 0.09 (0.39), residues: 181 loop : -0.91 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.006 0.001 HIS R 241 PHE 0.011 0.001 PHE A 212 TYR 0.009 0.001 TYR B 59 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 348) hydrogen bonds : angle 4.17826 ( 1020) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.46713 ( 2) covalent geometry : bond 0.00207 ( 6703) covalent geometry : angle 0.46466 ( 9177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.686 Fit side-chains REVERT: A 267 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7516 (tp-100) REVERT: B 155 ASN cc_start: 0.7990 (t0) cc_final: 0.7743 (t0) outliers start: 4 outliers final: 3 residues processed: 81 average time/residue: 0.1716 time to fit residues: 19.0279 Evaluate side-chains 77 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain R residue 143 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.095761 restraints weight = 35046.212| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 4.60 r_work: 0.2998 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6704 Z= 0.115 Angle : 0.473 7.634 9179 Z= 0.248 Chirality : 0.041 0.168 1103 Planarity : 0.003 0.037 1145 Dihedral : 10.256 178.562 990 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.54 % Allowed : 11.47 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.29), residues: 889 helix: 2.38 (0.27), residues: 410 sheet: 0.15 (0.39), residues: 181 loop : -0.89 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.006 0.001 HIS R 241 PHE 0.010 0.001 PHE A 212 TYR 0.012 0.001 TYR B 59 ARG 0.001 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 348) hydrogen bonds : angle 4.02260 ( 1020) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.35206 ( 2) covalent geometry : bond 0.00254 ( 6703) covalent geometry : angle 0.47308 ( 9177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.685 Fit side-chains REVERT: B 259 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8482 (pt0) outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 0.1905 time to fit residues: 22.5292 Evaluate side-chains 84 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 143 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 21 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 35 optimal weight: 0.1980 chunk 88 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098389 restraints weight = 32496.940| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 4.48 r_work: 0.3046 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6704 Z= 0.087 Angle : 0.444 7.481 9179 Z= 0.231 Chirality : 0.039 0.182 1103 Planarity : 0.003 0.037 1145 Dihedral : 10.149 178.976 990 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.20 % Allowed : 13.18 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.29), residues: 889 helix: 2.55 (0.27), residues: 404 sheet: 0.25 (0.40), residues: 181 loop : -0.89 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.006 0.001 HIS R 241 PHE 0.009 0.001 PHE A 212 TYR 0.006 0.001 TYR A 339 ARG 0.005 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 348) hydrogen bonds : angle 3.78653 ( 1020) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.46958 ( 2) covalent geometry : bond 0.00171 ( 6703) covalent geometry : angle 0.44378 ( 9177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.678 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 84 average time/residue: 0.1791 time to fit residues: 20.5882 Evaluate side-chains 75 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain R residue 236 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.0060 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 85 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099095 restraints weight = 27832.714| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 4.17 r_work: 0.3050 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6704 Z= 0.086 Angle : 0.439 7.502 9179 Z= 0.228 Chirality : 0.040 0.185 1103 Planarity : 0.003 0.035 1145 Dihedral : 10.074 178.855 990 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.37 % Allowed : 13.87 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.29), residues: 889 helix: 2.58 (0.27), residues: 405 sheet: 0.25 (0.40), residues: 181 loop : -0.83 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 211 HIS 0.006 0.001 HIS R 241 PHE 0.008 0.001 PHE A 212 TYR 0.009 0.001 TYR R 219 ARG 0.005 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 348) hydrogen bonds : angle 3.69570 ( 1020) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.42985 ( 2) covalent geometry : bond 0.00173 ( 6703) covalent geometry : angle 0.43934 ( 9177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.783 Fit side-chains REVERT: B 259 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8418 (pt0) outliers start: 8 outliers final: 7 residues processed: 86 average time/residue: 0.1855 time to fit residues: 21.8764 Evaluate side-chains 81 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.098348 restraints weight = 30886.945| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.35 r_work: 0.3034 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6704 Z= 0.091 Angle : 0.443 7.476 9179 Z= 0.229 Chirality : 0.040 0.189 1103 Planarity : 0.003 0.035 1145 Dihedral : 10.046 178.955 990 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.05 % Allowed : 14.55 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 889 helix: 2.57 (0.27), residues: 405 sheet: 0.22 (0.39), residues: 181 loop : -0.82 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 339 HIS 0.006 0.001 HIS R 241 PHE 0.008 0.001 PHE A 212 TYR 0.007 0.001 TYR A 339 ARG 0.004 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 348) hydrogen bonds : angle 3.67701 ( 1020) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.37373 ( 2) covalent geometry : bond 0.00192 ( 6703) covalent geometry : angle 0.44278 ( 9177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.724 Fit side-chains REVERT: B 259 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8492 (pt0) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.1770 time to fit residues: 20.8631 Evaluate side-chains 84 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 84 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096995 restraints weight = 34155.033| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 4.54 r_work: 0.3010 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6704 Z= 0.101 Angle : 0.450 7.450 9179 Z= 0.234 Chirality : 0.040 0.197 1103 Planarity : 0.003 0.035 1145 Dihedral : 10.043 178.911 990 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.23 % Allowed : 14.73 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.29), residues: 889 helix: 2.57 (0.27), residues: 404 sheet: 0.18 (0.39), residues: 181 loop : -0.85 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.007 0.001 HIS R 241 PHE 0.008 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.004 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 348) hydrogen bonds : angle 3.71034 ( 1020) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.32196 ( 2) covalent geometry : bond 0.00222 ( 6703) covalent geometry : angle 0.45035 ( 9177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.742 Fit side-chains REVERT: A 349 SER cc_start: 0.9153 (p) cc_final: 0.8870 (p) REVERT: B 259 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8498 (pt0) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.1737 time to fit residues: 20.9709 Evaluate side-chains 87 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 57 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096944 restraints weight = 41375.578| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 5.23 r_work: 0.2986 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6704 Z= 0.102 Angle : 0.454 7.988 9179 Z= 0.235 Chirality : 0.040 0.191 1103 Planarity : 0.003 0.035 1145 Dihedral : 10.044 178.893 990 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.40 % Allowed : 14.73 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.29), residues: 889 helix: 2.59 (0.27), residues: 404 sheet: 0.17 (0.39), residues: 181 loop : -0.85 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.007 0.001 HIS R 241 PHE 0.008 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.003 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 348) hydrogen bonds : angle 3.71077 ( 1020) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.34648 ( 2) covalent geometry : bond 0.00227 ( 6703) covalent geometry : angle 0.45426 ( 9177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.698 Fit side-chains REVERT: A 349 SER cc_start: 0.9129 (p) cc_final: 0.8874 (p) REVERT: B 259 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8498 (pt0) outliers start: 14 outliers final: 11 residues processed: 89 average time/residue: 0.1674 time to fit residues: 20.5122 Evaluate side-chains 88 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 83 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 64 optimal weight: 0.0570 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.097953 restraints weight = 24144.080| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.86 r_work: 0.3036 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6704 Z= 0.100 Angle : 0.454 8.395 9179 Z= 0.235 Chirality : 0.040 0.208 1103 Planarity : 0.003 0.035 1145 Dihedral : 10.035 178.797 990 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.88 % Allowed : 15.24 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 889 helix: 2.60 (0.27), residues: 404 sheet: 0.19 (0.39), residues: 181 loop : -0.84 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 211 HIS 0.007 0.001 HIS R 241 PHE 0.008 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.004 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 348) hydrogen bonds : angle 3.70042 ( 1020) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.36512 ( 2) covalent geometry : bond 0.00219 ( 6703) covalent geometry : angle 0.45358 ( 9177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.812 Fit side-chains REVERT: A 349 SER cc_start: 0.9092 (p) cc_final: 0.8855 (p) REVERT: B 259 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8476 (pt0) outliers start: 11 outliers final: 9 residues processed: 86 average time/residue: 0.1824 time to fit residues: 21.6439 Evaluate side-chains 85 residues out of total 783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 236 SER Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.0370 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097287 restraints weight = 25895.626| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.83 r_work: 0.3041 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6704 Z= 0.150 Angle : 0.496 8.767 9179 Z= 0.259 Chirality : 0.041 0.200 1103 Planarity : 0.003 0.035 1145 Dihedral : 10.103 178.575 990 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.88 % Allowed : 15.58 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 889 helix: 2.46 (0.27), residues: 410 sheet: 0.16 (0.38), residues: 186 loop : -0.79 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.007 0.001 HIS R 241 PHE 0.011 0.001 PHE R 289 TYR 0.009 0.001 TYR A 339 ARG 0.003 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.04734 ( 348) hydrogen bonds : angle 3.88574 ( 1020) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.18559 ( 2) covalent geometry : bond 0.00358 ( 6703) covalent geometry : angle 0.49592 ( 9177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3567.20 seconds wall clock time: 62 minutes 30.33 seconds (3750.33 seconds total)