Starting phenix.real_space_refine on Thu Sep 18 11:05:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnx_45765/09_2025/9cnx_45765.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnx_45765/09_2025/9cnx_45765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cnx_45765/09_2025/9cnx_45765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnx_45765/09_2025/9cnx_45765.map" model { file = "/net/cci-nas-00/data/ceres_data/9cnx_45765/09_2025/9cnx_45765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnx_45765/09_2025/9cnx_45765.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5743 atoms to isotropic. 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 Zn 1 6.06 5 S 31 5.16 5 C 7303 2.51 5 N 1986 2.21 5 O 2261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11582 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 6025 Classifications: {'peptide': 762} Link IDs: {'PTRANS': 28, 'TRANS': 733} Chain breaks: 1 Chain: "B" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2657 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 11, 'TRANS': 341} Chain breaks: 1 Chain: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 385 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 6, 'TRANS': 47} Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1703 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain breaks: 1 Chain: "E" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 691 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "G" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 119 Unusual residues: {'ACY': 1} Classifications: {'peptide': 13, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="ACY G 0 " pdbres="PHE G 1 " Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 12 Planarities with less than four sites: {'ACY:plan-1': 1, 'ABA:plan-1': 1, 'ALN:plan-2': 1, 'YNM:plan-2': 1, 'MHS:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.43, per 1000 atoms: 0.21 Number of scatterers: 11582 At special positions: 0 Unit cell: (124.8, 126, 151.2, 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) Zn 1 29.99 S 31 16.00 O 2261 8.00 N 1986 7.00 C 7303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 541.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 901 " pdb="ZN ZN G 901 " - pdb=" NE2 MHS G 11 " pdb="ZN ZN G 901 " - pdb=" ND1 HIS G 4 " pdb="ZN ZN G 901 " - pdb=" NE2 HIS G 9 " 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2702 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 16 sheets defined 25.3% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 70 removed outlier: 4.035A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.958A pdb=" N GLY A 118 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.564A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.508A pdb=" N LYS A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 314 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.740A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 removed outlier: 3.814A pdb=" N LEU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.740A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.869A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 removed outlier: 3.547A pdb=" N VAL A 733 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 754 removed outlier: 3.668A pdb=" N GLN A 753 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 39 removed outlier: 3.749A pdb=" N SER C 36 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.657A pdb=" N ALA C 79 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 80' Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.954A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.942A pdb=" N ARG D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.672A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.829A pdb=" N ASP D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.507A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.834A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.407A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.596A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.564A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 7.366A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 273 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 341 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY A 275 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.744A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 433 removed outlier: 3.759A pdb=" N TYR A 574 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 738 " --> pdb=" O GLY A 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 771 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.872A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68 removed outlier: 7.234A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.672A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.731A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.917A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.928A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.566A pdb=" N VAL B 305 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.512A pdb=" N TRP B 348 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.686A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.686A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1377 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: 1.86 Time building geometry restraints manager: 1.27 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: 3857 1.34 - 1.46: 2158 1.46 - 1.57: 5755 1.57 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 11831 Sorted by residual: bond pdb=" ND1 MHS G 11 " pdb=" CE1 MHS G 11 " ideal model delta sigma weight residual 1.351 1.399 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" CE1 MHS G 11 " pdb=" NE2 MHS G 11 " ideal model delta sigma weight residual 1.307 1.349 -0.042 2.00e-02 2.50e+03 4.34e+00 bond pdb=" CG MHS G 11 " pdb=" CD2 MHS G 11 " ideal model delta sigma weight residual 1.370 1.408 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C ACY G 0 " pdb=" O ACY G 0 " ideal model delta sigma weight residual 1.248 1.286 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" CA VAL D 27 " pdb=" C VAL D 27 " ideal model delta sigma weight residual 1.525 1.560 -0.035 2.10e-02 2.27e+03 2.72e+00 ... (remaining 11826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 15807 2.24 - 4.49: 222 4.49 - 6.73: 30 6.73 - 8.97: 10 8.97 - 11.21: 3 Bond angle restraints: 16072 Sorted by residual: angle pdb=" N GLU D 56 " pdb=" CA GLU D 56 " pdb=" CB GLU D 56 " ideal model delta sigma weight residual 110.28 117.40 -7.12 1.55e+00 4.16e-01 2.11e+01 angle pdb=" N ARG G 7 " pdb=" CA ARG G 7 " pdb=" C ARG G 7 " ideal model delta sigma weight residual 111.00 122.21 -11.21 2.80e+00 1.28e-01 1.60e+01 angle pdb=" C ASN D 33 " pdb=" N GLU D 34 " pdb=" CA GLU D 34 " ideal model delta sigma weight residual 122.06 115.15 6.91 1.86e+00 2.89e-01 1.38e+01 angle pdb=" C LEU D 55 " pdb=" N GLU D 56 " pdb=" CA GLU D 56 " ideal model delta sigma weight residual 120.31 114.75 5.56 1.52e+00 4.33e-01 1.34e+01 angle pdb=" CA MET D 109 " pdb=" CB MET D 109 " pdb=" CG MET D 109 " ideal model delta sigma weight residual 114.10 121.15 -7.05 2.00e+00 2.50e-01 1.24e+01 ... (remaining 16067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 6481 17.75 - 35.51: 394 35.51 - 53.26: 69 53.26 - 71.01: 17 71.01 - 88.77: 13 Dihedral angle restraints: 6974 sinusoidal: 2726 harmonic: 4248 Sorted by residual: dihedral pdb=" CA GLN A 495 " pdb=" C GLN A 495 " pdb=" N ALA A 496 " pdb=" CA ALA A 496 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA HIS B 324 " pdb=" C HIS B 324 " pdb=" N ARG B 325 " pdb=" CA ARG B 325 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA TRP A 546 " pdb=" C TRP A 546 " pdb=" N ARG A 547 " pdb=" CA ARG A 547 " ideal model delta harmonic sigma weight residual 180.00 163.65 16.35 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 6971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1228 0.045 - 0.090: 367 0.090 - 0.135: 140 0.135 - 0.180: 14 0.180 - 0.225: 4 Chirality restraints: 1753 Sorted by residual: chirality pdb=" CB ILE A 94 " pdb=" CA ILE A 94 " pdb=" CG1 ILE A 94 " pdb=" CG2 ILE A 94 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ARG G 7 " pdb=" N ARG G 7 " pdb=" C ARG G 7 " pdb=" CB ARG G 7 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL E 27 " pdb=" CA VAL E 27 " pdb=" CG1 VAL E 27 " pdb=" CG2 VAL E 27 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1750 not shown) Planarity restraints: 2111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 91 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A 92 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 675 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 676 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 248 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 249 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 249 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 249 " 0.026 5.00e-02 4.00e+02 ... (remaining 2108 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3563 2.83 - 3.35: 10080 3.35 - 3.86: 17493 3.86 - 4.38: 19747 4.38 - 4.90: 36269 Nonbonded interactions: 87152 Sorted by model distance: nonbonded pdb=" NH1 ARG A 79 " pdb=" O ASP A 80 " model vdw 2.310 3.120 nonbonded pdb=" ND1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 2.331 3.120 nonbonded pdb=" OG1 THR B 309 " pdb=" O GLY B 312 " model vdw 2.342 3.040 nonbonded pdb=" OE1 GLN B 319 " pdb=" NH2 ARG B 355 " model vdw 2.344 3.120 nonbonded pdb=" NE2 GLN D 230 " pdb=" OD1 ASP E 66 " model vdw 2.352 3.120 ... (remaining 87147 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.900 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.008 0.512 11837 Z= 0.290 Angle : 0.704 11.214 16072 Z= 0.371 Chirality : 0.049 0.225 1753 Planarity : 0.005 0.058 2111 Dihedral : 12.672 88.768 4272 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.21), residues: 1454 helix: 0.70 (0.28), residues: 311 sheet: 0.41 (0.24), residues: 445 loop : -0.24 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 49 TYR 0.013 0.001 TYR B 123 PHE 0.026 0.002 PHE A 428 TRP 0.021 0.002 TRP B 93 HIS 0.006 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00345 (11831) covalent geometry : angle 0.70383 (16072) hydrogen bonds : bond 0.20283 ( 496) hydrogen bonds : angle 7.17670 ( 1377) metal coordination : bond 0.41581 ( 3) Misc. bond : bond 0.05802 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.9129 (mtp) cc_final: 0.8898 (tpt) REVERT: A 304 MET cc_start: 0.8080 (ttp) cc_final: 0.7861 (ttm) REVERT: A 369 MET cc_start: 0.8647 (mmp) cc_final: 0.8328 (mmp) REVERT: A 459 ASN cc_start: 0.7693 (t0) cc_final: 0.7454 (t0) REVERT: B 48 TRP cc_start: 0.8592 (p-90) cc_final: 0.7676 (p-90) REVERT: D 35 ILE cc_start: 0.9057 (mt) cc_final: 0.8707 (mt) REVERT: D 87 LEU cc_start: 0.9285 (mp) cc_final: 0.9003 (mp) REVERT: E 44 SER cc_start: 0.8788 (p) cc_final: 0.8432 (p) REVERT: E 47 ARG cc_start: 0.7416 (mpt180) cc_final: 0.7080 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1071 time to fit residues: 20.0936 Evaluate side-chains 109 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.102438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.074731 restraints weight = 24539.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.074902 restraints weight = 23122.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075254 restraints weight = 25775.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.075929 restraints weight = 15523.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.076539 restraints weight = 13526.578| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.328 11837 Z= 0.223 Angle : 0.596 10.354 16072 Z= 0.320 Chirality : 0.045 0.199 1753 Planarity : 0.005 0.058 2111 Dihedral : 5.203 69.579 1623 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.73 % Allowed : 4.45 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.21), residues: 1454 helix: 1.06 (0.29), residues: 311 sheet: 0.51 (0.23), residues: 456 loop : -0.29 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 25 TYR 0.013 0.002 TYR D 36 PHE 0.014 0.001 PHE E 77 TRP 0.016 0.001 TRP A 776 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00456 (11831) covalent geometry : angle 0.59594 (16072) hydrogen bonds : bond 0.05801 ( 496) hydrogen bonds : angle 5.33852 ( 1377) metal coordination : bond 0.18915 ( 3) Misc. bond : bond 0.00028 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 304 MET cc_start: 0.8146 (ttp) cc_final: 0.7924 (ttm) REVERT: A 369 MET cc_start: 0.8814 (mmp) cc_final: 0.8602 (mmp) REVERT: B 48 TRP cc_start: 0.8607 (p-90) cc_final: 0.7727 (p-90) REVERT: B 189 MET cc_start: 0.8464 (tpp) cc_final: 0.7745 (tpp) REVERT: B 278 MET cc_start: 0.7668 (mpp) cc_final: 0.7338 (mpp) REVERT: D 42 LYS cc_start: 0.8680 (mtmm) cc_final: 0.8044 (mtmm) REVERT: D 49 ARG cc_start: 0.7622 (mmm-85) cc_final: 0.7305 (tpp80) REVERT: D 87 LEU cc_start: 0.9037 (mp) cc_final: 0.8823 (mp) REVERT: D 183 GLU cc_start: 0.7569 (tt0) cc_final: 0.7345 (tt0) REVERT: E 44 SER cc_start: 0.8765 (p) cc_final: 0.8470 (p) REVERT: E 96 ASN cc_start: 0.8319 (t0) cc_final: 0.7831 (p0) outliers start: 9 outliers final: 6 residues processed: 118 average time/residue: 0.1003 time to fit residues: 17.3936 Evaluate side-chains 116 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 97 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.101732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073751 restraints weight = 24821.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.072475 restraints weight = 22719.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.073494 restraints weight = 21084.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.074433 restraints weight = 15453.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.074705 restraints weight = 14089.905| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11837 Z= 0.217 Angle : 0.588 9.506 16072 Z= 0.314 Chirality : 0.045 0.181 1753 Planarity : 0.005 0.080 2111 Dihedral : 5.179 70.732 1623 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.81 % Allowed : 7.44 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.22), residues: 1454 helix: 1.29 (0.30), residues: 305 sheet: 0.30 (0.23), residues: 472 loop : -0.31 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 25 TYR 0.016 0.002 TYR B 345 PHE 0.024 0.001 PHE A 426 TRP 0.013 0.001 TRP A 776 HIS 0.004 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00501 (11831) covalent geometry : angle 0.58774 (16072) hydrogen bonds : bond 0.05554 ( 496) hydrogen bonds : angle 5.08779 ( 1377) metal coordination : bond 0.00371 ( 3) Misc. bond : bond 0.00026 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.446 Fit side-chains REVERT: B 48 TRP cc_start: 0.8613 (p-90) cc_final: 0.7611 (p-90) REVERT: D 49 ARG cc_start: 0.7732 (mmm-85) cc_final: 0.7338 (tpp80) REVERT: D 183 GLU cc_start: 0.7608 (tt0) cc_final: 0.7343 (tt0) REVERT: E 96 ASN cc_start: 0.8373 (t0) cc_final: 0.7861 (p0) outliers start: 10 outliers final: 6 residues processed: 119 average time/residue: 0.1034 time to fit residues: 18.0214 Evaluate side-chains 114 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 111 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 111 optimal weight: 3.9990 chunk 104 optimal weight: 0.0570 chunk 9 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.102919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.074626 restraints weight = 24649.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.073367 restraints weight = 17833.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074163 restraints weight = 16334.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.074716 restraints weight = 13260.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.075045 restraints weight = 12525.533| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11837 Z= 0.148 Angle : 0.540 8.319 16072 Z= 0.286 Chirality : 0.043 0.145 1753 Planarity : 0.004 0.072 2111 Dihedral : 4.935 71.019 1623 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.21 % Allowed : 8.66 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.22), residues: 1454 helix: 1.59 (0.30), residues: 306 sheet: 0.34 (0.23), residues: 474 loop : -0.26 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 47 TYR 0.020 0.001 TYR B 333 PHE 0.012 0.001 PHE A 494 TRP 0.013 0.001 TRP A 546 HIS 0.003 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00336 (11831) covalent geometry : angle 0.54038 (16072) hydrogen bonds : bond 0.04603 ( 496) hydrogen bonds : angle 4.80592 ( 1377) metal coordination : bond 0.00502 ( 3) Misc. bond : bond 0.00013 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.461 Fit side-chains REVERT: B 32 MET cc_start: 0.7788 (ttm) cc_final: 0.7531 (ttt) REVERT: B 48 TRP cc_start: 0.8693 (p-90) cc_final: 0.7596 (p-90) REVERT: D 42 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8387 (mtmm) REVERT: D 49 ARG cc_start: 0.7941 (mmm-85) cc_final: 0.7434 (tpp80) REVERT: D 87 LEU cc_start: 0.9283 (mp) cc_final: 0.9080 (mp) REVERT: D 183 GLU cc_start: 0.7655 (tt0) cc_final: 0.7356 (tt0) REVERT: D 227 MET cc_start: 0.8439 (mtp) cc_final: 0.8068 (mtp) REVERT: E 41 ASN cc_start: 0.8317 (t0) cc_final: 0.8056 (t0) REVERT: E 47 ARG cc_start: 0.7565 (mpt180) cc_final: 0.7317 (mmt-90) outliers start: 15 outliers final: 12 residues processed: 124 average time/residue: 0.1055 time to fit residues: 19.3971 Evaluate side-chains 124 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 97 SER Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 118 optimal weight: 5.9990 chunk 71 optimal weight: 0.0370 chunk 77 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.100567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.071650 restraints weight = 24820.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.071100 restraints weight = 16226.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.072124 restraints weight = 13899.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.072456 restraints weight = 11408.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.073431 restraints weight = 10637.562| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 11837 Z= 0.386 Angle : 0.697 8.770 16072 Z= 0.370 Chirality : 0.048 0.187 1753 Planarity : 0.005 0.071 2111 Dihedral : 5.449 75.356 1623 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.02 % Allowed : 10.28 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.22), residues: 1454 helix: 1.28 (0.30), residues: 311 sheet: -0.02 (0.23), residues: 478 loop : -0.50 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 83 TYR 0.018 0.002 TYR B 333 PHE 0.024 0.002 PHE A 426 TRP 0.015 0.002 TRP B 348 HIS 0.005 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00894 (11831) covalent geometry : angle 0.69744 (16072) hydrogen bonds : bond 0.06673 ( 496) hydrogen bonds : angle 5.20052 ( 1377) metal coordination : bond 0.01327 ( 3) Misc. bond : bond 0.00039 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8262 (tpt) cc_final: 0.8046 (tpt) REVERT: A 261 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8663 (p) REVERT: B 32 MET cc_start: 0.8026 (ttm) cc_final: 0.7784 (ttt) REVERT: B 48 TRP cc_start: 0.8762 (p-90) cc_final: 0.7636 (p-90) REVERT: B 76 ASP cc_start: 0.7300 (t0) cc_final: 0.7073 (t0) REVERT: B 278 MET cc_start: 0.7989 (mpp) cc_final: 0.7332 (mpp) REVERT: B 333 TYR cc_start: 0.7417 (t80) cc_final: 0.7150 (t80) REVERT: D 42 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8599 (mtmm) REVERT: D 49 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7503 (tpp80) REVERT: D 183 GLU cc_start: 0.7710 (tt0) cc_final: 0.7487 (tt0) REVERT: D 227 MET cc_start: 0.8750 (mtp) cc_final: 0.8385 (mtp) REVERT: E 41 ASN cc_start: 0.8420 (t0) cc_final: 0.8209 (t0) REVERT: E 47 ARG cc_start: 0.7566 (mpt180) cc_final: 0.7366 (mmt-90) REVERT: E 96 ASN cc_start: 0.8462 (t0) cc_final: 0.7786 (p0) outliers start: 25 outliers final: 17 residues processed: 126 average time/residue: 0.1046 time to fit residues: 19.4758 Evaluate side-chains 128 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 111 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 139 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 121 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.104054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075920 restraints weight = 24786.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.075192 restraints weight = 16400.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.075608 restraints weight = 18052.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.076283 restraints weight = 12459.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.076864 restraints weight = 11032.869| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11837 Z= 0.129 Angle : 0.541 11.308 16072 Z= 0.286 Chirality : 0.043 0.141 1753 Planarity : 0.004 0.071 2111 Dihedral : 4.939 73.210 1623 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.05 % Allowed : 11.97 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.22), residues: 1454 helix: 1.72 (0.30), residues: 308 sheet: 0.25 (0.23), residues: 465 loop : -0.42 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 10 TYR 0.036 0.001 TYR A 142 PHE 0.012 0.001 PHE A 494 TRP 0.017 0.001 TRP A 546 HIS 0.004 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00288 (11831) covalent geometry : angle 0.54104 (16072) hydrogen bonds : bond 0.04406 ( 496) hydrogen bonds : angle 4.77786 ( 1377) metal coordination : bond 0.00433 ( 3) Misc. bond : bond 0.00024 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8260 (tpt) cc_final: 0.7994 (tpt) REVERT: A 142 TYR cc_start: 0.7789 (m-80) cc_final: 0.7525 (m-80) REVERT: B 48 TRP cc_start: 0.8729 (p-90) cc_final: 0.7642 (p-90) REVERT: B 76 ASP cc_start: 0.7345 (t0) cc_final: 0.7144 (t0) REVERT: D 42 LYS cc_start: 0.8764 (mtmm) cc_final: 0.8483 (mtmm) REVERT: D 49 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7442 (tpp80) REVERT: D 227 MET cc_start: 0.8352 (mtp) cc_final: 0.7956 (mtp) REVERT: E 28 TYR cc_start: 0.8404 (t80) cc_final: 0.8164 (t80) REVERT: E 41 ASN cc_start: 0.8373 (t0) cc_final: 0.8163 (t0) REVERT: E 54 GLN cc_start: 0.8415 (mt0) cc_final: 0.8126 (mt0) REVERT: E 96 ASN cc_start: 0.8343 (t0) cc_final: 0.7770 (p0) outliers start: 13 outliers final: 8 residues processed: 123 average time/residue: 0.0987 time to fit residues: 18.1709 Evaluate side-chains 120 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 51 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 26 optimal weight: 2.9990 chunk 114 optimal weight: 0.0670 chunk 17 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 119 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.103673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.074762 restraints weight = 24750.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.074194 restraints weight = 16523.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.075323 restraints weight = 14018.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.075616 restraints weight = 11417.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.076816 restraints weight = 10565.652| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11837 Z= 0.110 Angle : 0.528 11.157 16072 Z= 0.276 Chirality : 0.042 0.137 1753 Planarity : 0.004 0.070 2111 Dihedral : 4.697 71.970 1623 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.13 % Allowed : 12.30 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.22), residues: 1454 helix: 1.96 (0.30), residues: 311 sheet: 0.41 (0.23), residues: 470 loop : -0.30 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 47 TYR 0.038 0.001 TYR A 142 PHE 0.024 0.001 PHE A 426 TRP 0.017 0.001 TRP A 546 HIS 0.002 0.000 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00242 (11831) covalent geometry : angle 0.52818 (16072) hydrogen bonds : bond 0.03911 ( 496) hydrogen bonds : angle 4.55552 ( 1377) metal coordination : bond 0.00352 ( 3) Misc. bond : bond 0.00009 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8374 (tpt) cc_final: 0.8033 (tpt) REVERT: A 142 TYR cc_start: 0.7868 (m-80) cc_final: 0.7631 (m-80) REVERT: A 325 MET cc_start: 0.7220 (pmm) cc_final: 0.7008 (pmm) REVERT: A 384 GLN cc_start: 0.8001 (pt0) cc_final: 0.7561 (pt0) REVERT: B 48 TRP cc_start: 0.8741 (p-90) cc_final: 0.7647 (p-90) REVERT: D 49 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7515 (tpp80) REVERT: D 87 LEU cc_start: 0.9328 (mp) cc_final: 0.9088 (mp) REVERT: D 227 MET cc_start: 0.8289 (mtp) cc_final: 0.7892 (mtp) REVERT: E 28 TYR cc_start: 0.8377 (t80) cc_final: 0.8146 (t80) REVERT: E 41 ASN cc_start: 0.8450 (t0) cc_final: 0.8217 (t0) REVERT: E 47 ARG cc_start: 0.7586 (mpt180) cc_final: 0.7209 (mmt180) REVERT: E 54 GLN cc_start: 0.8494 (mt0) cc_final: 0.8179 (mt0) REVERT: E 96 ASN cc_start: 0.8369 (t0) cc_final: 0.7785 (p0) outliers start: 14 outliers final: 10 residues processed: 122 average time/residue: 0.1005 time to fit residues: 18.2577 Evaluate side-chains 118 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 145 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.074371 restraints weight = 24653.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.073936 restraints weight = 16052.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.074974 restraints weight = 13863.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.075330 restraints weight = 11241.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.075877 restraints weight = 10422.765| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11837 Z= 0.138 Angle : 0.549 10.113 16072 Z= 0.285 Chirality : 0.043 0.149 1753 Planarity : 0.004 0.070 2111 Dihedral : 4.668 71.219 1623 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.05 % Allowed : 12.86 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.22), residues: 1454 helix: 2.03 (0.30), residues: 311 sheet: 0.42 (0.23), residues: 471 loop : -0.28 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 83 TYR 0.035 0.001 TYR A 142 PHE 0.019 0.001 PHE A 428 TRP 0.016 0.001 TRP A 546 HIS 0.003 0.000 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00314 (11831) covalent geometry : angle 0.54870 (16072) hydrogen bonds : bond 0.04229 ( 496) hydrogen bonds : angle 4.55088 ( 1377) metal coordination : bond 0.00509 ( 3) Misc. bond : bond 0.00014 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8384 (tpt) cc_final: 0.8037 (tpt) REVERT: A 142 TYR cc_start: 0.7894 (m-80) cc_final: 0.7681 (m-80) REVERT: A 261 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8551 (p) REVERT: B 48 TRP cc_start: 0.8743 (p-90) cc_final: 0.7600 (p-90) REVERT: D 49 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7522 (tpp80) REVERT: D 87 LEU cc_start: 0.9334 (mp) cc_final: 0.9096 (mp) REVERT: E 41 ASN cc_start: 0.8384 (t0) cc_final: 0.8163 (t0) REVERT: E 54 GLN cc_start: 0.8511 (mt0) cc_final: 0.8195 (mt0) REVERT: E 96 ASN cc_start: 0.8385 (t0) cc_final: 0.7817 (p0) outliers start: 13 outliers final: 9 residues processed: 120 average time/residue: 0.1008 time to fit residues: 17.9509 Evaluate side-chains 119 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 55 optimal weight: 0.6980 chunk 97 optimal weight: 0.0980 chunk 120 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.103987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.074696 restraints weight = 24621.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.074207 restraints weight = 18017.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.074975 restraints weight = 15783.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075815 restraints weight = 12369.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.076084 restraints weight = 11251.255| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11837 Z= 0.120 Angle : 0.555 12.615 16072 Z= 0.284 Chirality : 0.043 0.136 1753 Planarity : 0.004 0.069 2111 Dihedral : 4.645 74.250 1623 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.97 % Allowed : 12.94 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.22), residues: 1454 helix: 2.04 (0.30), residues: 314 sheet: 0.48 (0.23), residues: 472 loop : -0.25 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 83 TYR 0.034 0.001 TYR A 142 PHE 0.019 0.001 PHE A 428 TRP 0.015 0.001 TRP A 546 HIS 0.002 0.000 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00269 (11831) covalent geometry : angle 0.55540 (16072) hydrogen bonds : bond 0.04021 ( 496) hydrogen bonds : angle 4.50991 ( 1377) metal coordination : bond 0.00373 ( 3) Misc. bond : bond 0.00110 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8230 (tpt) cc_final: 0.7975 (tpt) REVERT: A 142 TYR cc_start: 0.7770 (m-80) cc_final: 0.7535 (m-80) REVERT: A 261 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8538 (p) REVERT: B 48 TRP cc_start: 0.8726 (p-90) cc_final: 0.7622 (p-90) REVERT: D 49 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7437 (tpp80) REVERT: D 87 LEU cc_start: 0.9294 (mp) cc_final: 0.9089 (mp) REVERT: E 41 ASN cc_start: 0.8388 (t0) cc_final: 0.8169 (t0) REVERT: E 54 GLN cc_start: 0.8499 (mt0) cc_final: 0.8183 (mt0) REVERT: E 96 ASN cc_start: 0.8352 (t0) cc_final: 0.7847 (p0) outliers start: 12 outliers final: 10 residues processed: 118 average time/residue: 0.1010 time to fit residues: 17.7038 Evaluate side-chains 119 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 62 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.0870 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 GLN ** G 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.105743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.070133 restraints weight = 24724.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072909 restraints weight = 13700.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074648 restraints weight = 9698.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075700 restraints weight = 7924.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.076400 restraints weight = 7003.257| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11837 Z= 0.108 Angle : 0.553 13.511 16072 Z= 0.282 Chirality : 0.042 0.134 1753 Planarity : 0.004 0.069 2111 Dihedral : 4.483 70.891 1623 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.73 % Allowed : 13.67 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.22), residues: 1454 helix: 2.15 (0.30), residues: 315 sheet: 0.55 (0.23), residues: 472 loop : -0.19 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 83 TYR 0.032 0.001 TYR A 142 PHE 0.021 0.001 PHE A 426 TRP 0.014 0.001 TRP A 546 HIS 0.002 0.000 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00241 (11831) covalent geometry : angle 0.55259 (16072) hydrogen bonds : bond 0.03703 ( 496) hydrogen bonds : angle 4.39204 ( 1377) metal coordination : bond 0.00298 ( 3) Misc. bond : bond 0.00128 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8708 (tpt) cc_final: 0.8328 (tpt) REVERT: A 142 TYR cc_start: 0.7911 (m-80) cc_final: 0.7618 (m-80) REVERT: A 261 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8506 (p) REVERT: B 48 TRP cc_start: 0.8619 (p-90) cc_final: 0.7596 (p-90) REVERT: D 42 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8343 (mtmm) REVERT: D 49 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7460 (tpp80) REVERT: D 87 LEU cc_start: 0.9322 (mp) cc_final: 0.9104 (mp) REVERT: E 28 TYR cc_start: 0.8232 (t80) cc_final: 0.7984 (t80) REVERT: E 41 ASN cc_start: 0.8147 (t0) cc_final: 0.7753 (t0) REVERT: E 45 LYS cc_start: 0.8898 (mtmm) cc_final: 0.8528 (mtmm) REVERT: E 96 ASN cc_start: 0.8126 (t0) cc_final: 0.7797 (p0) outliers start: 9 outliers final: 8 residues processed: 118 average time/residue: 0.1014 time to fit residues: 17.5603 Evaluate side-chains 115 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 718 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 86 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.075543 restraints weight = 24812.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075011 restraints weight = 16835.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.075338 restraints weight = 19381.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.076170 restraints weight = 13208.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076635 restraints weight = 11314.998| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11837 Z= 0.166 Angle : 0.581 14.045 16072 Z= 0.298 Chirality : 0.043 0.136 1753 Planarity : 0.004 0.068 2111 Dihedral : 4.618 72.272 1623 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.21 % Allowed : 12.70 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.22), residues: 1454 helix: 1.95 (0.30), residues: 316 sheet: 0.43 (0.23), residues: 473 loop : -0.24 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 83 TYR 0.031 0.001 TYR A 142 PHE 0.018 0.001 PHE A 428 TRP 0.013 0.001 TRP A 546 HIS 0.004 0.001 HIS G 9 Details of bonding type rmsd covalent geometry : bond 0.00384 (11831) covalent geometry : angle 0.58058 (16072) hydrogen bonds : bond 0.04487 ( 496) hydrogen bonds : angle 4.54463 ( 1377) metal coordination : bond 0.00592 ( 3) Misc. bond : bond 0.00115 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1856.92 seconds wall clock time: 32 minutes 48.16 seconds (1968.16 seconds total)