Starting phenix.real_space_refine on Sun May 25 05:51:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hg9_52131/05_2025/9hg9_52131.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hg9_52131/05_2025/9hg9_52131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hg9_52131/05_2025/9hg9_52131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hg9_52131/05_2025/9hg9_52131.map" model { file = "/net/cci-nas-00/data/ceres_data/9hg9_52131/05_2025/9hg9_52131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hg9_52131/05_2025/9hg9_52131.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 1 5.21 5 S 43 5.16 5 C 8417 2.51 5 N 2313 2.21 5 O 2632 1.98 5 H 12929 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26335 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 12165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 12165 Classifications: {'peptide': 787} Link IDs: {'PTRANS': 29, 'TRANS': 757} Chain: "B" Number of atoms: 5519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5519 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 11, 'TRANS': 358} Chain: "C" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 845 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "D" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3348 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1345 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "F" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2986 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 1 Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 126 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'UX8:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.47, per 1000 atoms: 0.51 Number of scatterers: 26335 At special positions: 0 Unit cell: (102.93, 126.29, 140.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 43 16.00 Mg 1 11.99 O 2632 8.00 N 2313 7.00 C 8417 6.00 H 12929 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.88 Conformation dependent library (CDL) restraints added in 2.6 seconds 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3146 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 20 sheets defined 29.6% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.810A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 315 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.663A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.891A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.822A pdb=" N GLY A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.551A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 695 Processing helix chain 'A' and resid 729 through 731 No H-bonds generated for 'chain 'A' and resid 729 through 731' Processing helix chain 'C' and resid 31 through 38 removed outlier: 3.811A pdb=" N VAL C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.546A pdb=" N GLY D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.712A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 105 through 121 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.617A pdb=" N VAL D 195 " --> pdb=" O TRP D 191 " (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 242 removed outlier: 3.656A pdb=" N ASN D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 27 removed outlier: 3.837A pdb=" N VAL E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'F' and resid 39 through 56 removed outlier: 3.779A pdb=" N GLN F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA F 56 " --> pdb=" O ASN F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 60 Processing helix chain 'F' and resid 63 through 88 Processing helix chain 'F' and resid 92 through 101 removed outlier: 3.644A pdb=" N ALA F 101 " --> pdb=" O ASP F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 118 removed outlier: 3.645A pdb=" N ARG F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 118 " --> pdb=" O MET F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 149 removed outlier: 4.272A pdb=" N TYR F 128 " --> pdb=" O ASN F 124 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG F 129 " --> pdb=" O TYR F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 167 removed outlier: 3.859A pdb=" N VAL F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 90 removed outlier: 7.058A pdb=" N GLN A 87 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 75 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS A 89 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 79 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN F 23 " --> pdb=" O ARG A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.179A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.506A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N SER B 193 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL A 245 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.012A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU A 268 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU A 337 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY A 270 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 339 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.012A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU A 268 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU A 337 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY A 270 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 339 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.518A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 485 Processing sheet with id=AA8, first strand: chain 'A' and resid 484 through 485 removed outlier: 3.507A pdb=" N VAL A 599 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR A 574 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.424A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 44 through 50 removed outlier: 5.135A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 67 removed outlier: 6.749A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 117 removed outlier: 6.590A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.906A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 201 through 202 removed outlier: 3.610A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.578A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 290 through 292 removed outlier: 4.082A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 331 through 333 removed outlier: 5.612A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.162A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AC2, first strand: chain 'F' and resid 35 through 38 624 hydrogen bonds defined for protein. 1755 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: 10.08 Time building geometry restraints manager: 9.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12929 1.03 - 1.23: 5 1.23 - 1.42: 5868 1.42 - 1.62: 7720 1.62 - 1.81: 84 Bond restraints: 26606 Sorted by residual: bond pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " ideal model delta sigma weight residual 1.525 1.351 0.174 2.10e-02 2.27e+03 6.88e+01 bond pdb=" N UX8 G 3 " pdb=" H UX8 G 3 " ideal model delta sigma weight residual 0.860 1.000 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" NE1 UX8 G 3 " pdb=" HE1 UX8 G 3 " ideal model delta sigma weight residual 0.860 1.000 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" CE3 UX8 G 3 " pdb=" HE3 UX8 G 3 " ideal model delta sigma weight residual 0.930 1.000 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CZ2 UX8 G 3 " pdb=" HZ2 UX8 G 3 " ideal model delta sigma weight residual 0.930 1.000 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 26601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 47628 2.24 - 4.47: 189 4.47 - 6.71: 17 6.71 - 8.94: 3 8.94 - 11.18: 3 Bond angle restraints: 47840 Sorted by residual: angle pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " pdb=" O UX8 G 3 " ideal model delta sigma weight residual 120.80 129.85 -9.05 1.70e+00 3.46e-01 2.83e+01 angle pdb=" CA ASP A 512 " pdb=" CB ASP A 512 " pdb=" CG ASP A 512 " ideal model delta sigma weight residual 112.60 117.09 -4.49 1.00e+00 1.00e+00 2.01e+01 angle pdb=" CB MET A 109 " pdb=" CG MET A 109 " pdb=" SD MET A 109 " ideal model delta sigma weight residual 112.70 123.88 -11.18 3.00e+00 1.11e-01 1.39e+01 angle pdb=" CB MET F 46 " pdb=" CG MET F 46 " pdb=" SD MET F 46 " ideal model delta sigma weight residual 112.70 122.21 -9.51 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CB LYS F 50 " pdb=" CG LYS F 50 " pdb=" CD LYS F 50 " ideal model delta sigma weight residual 111.30 117.95 -6.65 2.30e+00 1.89e-01 8.37e+00 ... (remaining 47835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 11439 17.31 - 34.63: 772 34.63 - 51.94: 280 51.94 - 69.26: 81 69.26 - 86.57: 10 Dihedral angle restraints: 12582 sinusoidal: 6824 harmonic: 5758 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -125.57 39.57 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" CA GLU A 689 " pdb=" C GLU A 689 " pdb=" N CYS A 690 " pdb=" CA CYS A 690 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CG ARG D 94 " pdb=" CD ARG D 94 " pdb=" NE ARG D 94 " pdb=" CZ ARG D 94 " ideal model delta sinusoidal sigma weight residual -90.00 -40.27 -49.73 2 1.50e+01 4.44e-03 1.24e+01 ... (remaining 12579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1803 0.062 - 0.125: 222 0.125 - 0.187: 5 0.187 - 0.249: 0 0.249 - 0.311: 1 Chirality restraints: 2031 Sorted by residual: chirality pdb=" CA UX8 G 3 " pdb=" N UX8 G 3 " pdb=" C UX8 G 3 " pdb=" CB UX8 G 3 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA LYS E 107 " pdb=" N LYS E 107 " pdb=" C LYS E 107 " pdb=" CB LYS E 107 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA VAL A 673 " pdb=" N VAL A 673 " pdb=" C VAL A 673 " pdb=" CB VAL A 673 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 2028 not shown) Planarity restraints: 4074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 512 " 0.011 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" N VAL A 513 " -0.035 2.00e-02 2.50e+03 pdb=" CA VAL A 513 " 0.009 2.00e-02 2.50e+03 pdb=" H VAL A 513 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 94 " 0.159 9.50e-02 1.11e+02 5.34e-02 3.49e+00 pdb=" NE ARG D 94 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D 94 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 94 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 94 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG D 94 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG D 94 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 94 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 94 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 154 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO B 155 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 155 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 155 " 0.018 5.00e-02 4.00e+02 ... (remaining 4071 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1087 2.18 - 2.78: 51751 2.78 - 3.39: 70809 3.39 - 3.99: 93559 3.99 - 4.60: 145530 Nonbonded interactions: 362736 Sorted by model distance: nonbonded pdb=" OE1 GLU C 39 " pdb=" H GLU C 39 " model vdw 1.574 2.450 nonbonded pdb=" OE1 GLU B 27 " pdb=" H GLU B 27 " model vdw 1.604 2.450 nonbonded pdb=" O LEU A 66 " pdb=" HG1 THR A 69 " model vdw 1.616 2.450 nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.617 2.450 nonbonded pdb=" O VAL D 27 " pdb="HH22 ARG D 61 " model vdw 1.625 2.450 ... (remaining 362731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.500 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 58.980 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.080 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:10.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 : 0.003 0.174 13680 Z= 0.142 Angle : 0.508 11.180 18571 Z= 0.266 Chirality : 0.041 0.311 2031 Planarity : 0.003 0.070 2448 Dihedral : 13.877 86.572 4997 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.28 % Allowed : 13.77 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1687 helix: 2.47 (0.24), residues: 454 sheet: 0.27 (0.25), residues: 462 loop : -0.40 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 348 HIS 0.001 0.000 HIS D 102 PHE 0.006 0.001 PHE A 67 TYR 0.016 0.001 TYR D 184 ARG 0.011 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.18298 ( 613) hydrogen bonds : angle 6.93174 ( 1755) SS BOND : bond 0.00057 ( 1) SS BOND : angle 2.95800 ( 2) covalent geometry : bond 0.00288 (13677) covalent geometry : angle 0.50669 (18569) Misc. bond : bond 0.02984 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.8715 (ttp-170) cc_final: 0.8379 (tmm-80) REVERT: E 46 ILE cc_start: 0.7466 (pp) cc_final: 0.7165 (pp) REVERT: F 416 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8426 (tm-30) outliers start: 4 outliers final: 2 residues processed: 150 average time/residue: 2.8260 time to fit residues: 462.3041 Evaluate side-chains 122 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain D residue 134 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 427 ASN A 441 GLN B 58 ASN B 276 GLN F 393 GLN G 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.101630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069454 restraints weight = 66063.869| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.74 r_work: 0.2807 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13680 Z= 0.173 Angle : 0.507 6.811 18571 Z= 0.271 Chirality : 0.042 0.150 2031 Planarity : 0.003 0.035 2448 Dihedral : 3.980 44.617 1878 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.90 % Allowed : 13.14 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1687 helix: 2.33 (0.24), residues: 461 sheet: 0.23 (0.25), residues: 466 loop : -0.46 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 776 HIS 0.004 0.001 HIS B 347 PHE 0.015 0.001 PHE A 517 TYR 0.015 0.001 TYR D 184 ARG 0.004 0.000 ARG A 526 Details of bonding type rmsd hydrogen bonds : bond 0.05045 ( 613) hydrogen bonds : angle 5.13709 ( 1755) SS BOND : bond 0.00377 ( 1) SS BOND : angle 2.74027 ( 2) covalent geometry : bond 0.00385 (13677) covalent geometry : angle 0.50657 (18569) Misc. bond : bond 0.00156 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8734 (tp30) cc_final: 0.8367 (tp30) REVERT: B 311 ASP cc_start: 0.9365 (m-30) cc_final: 0.9037 (t0) REVERT: E 83 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7311 (p90) outliers start: 13 outliers final: 3 residues processed: 143 average time/residue: 2.4211 time to fit residues: 383.2269 Evaluate side-chains 123 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 83 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 15 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.102722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.070449 restraints weight = 66660.559| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.78 r_work: 0.2764 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13680 Z= 0.200 Angle : 0.499 5.580 18571 Z= 0.266 Chirality : 0.042 0.144 2031 Planarity : 0.003 0.046 2448 Dihedral : 3.828 25.614 1875 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.46 % Allowed : 13.21 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1687 helix: 2.27 (0.24), residues: 462 sheet: 0.07 (0.24), residues: 471 loop : -0.47 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.002 0.001 HIS B 347 PHE 0.014 0.001 PHE A 517 TYR 0.014 0.001 TYR D 184 ARG 0.011 0.000 ARG A 120 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 613) hydrogen bonds : angle 4.86557 ( 1755) SS BOND : bond 0.00363 ( 1) SS BOND : angle 2.67456 ( 2) covalent geometry : bond 0.00450 (13677) covalent geometry : angle 0.49799 (18569) Misc. bond : bond 0.00078 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 GLN cc_start: 0.8611 (tt0) cc_final: 0.8300 (tm-30) REVERT: B 311 ASP cc_start: 0.9382 (m-30) cc_final: 0.9066 (t0) REVERT: E 83 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7193 (p90) REVERT: F 86 LYS cc_start: 0.9497 (tptp) cc_final: 0.9279 (tptp) REVERT: F 128 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6424 (t80) outliers start: 21 outliers final: 8 residues processed: 142 average time/residue: 2.3898 time to fit residues: 375.8258 Evaluate side-chains 133 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 83 HIS Chi-restraints excluded: chain F residue 128 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 0.0040 chunk 35 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.103547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.071356 restraints weight = 66472.685| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.79 r_work: 0.2787 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13680 Z= 0.115 Angle : 0.474 6.235 18571 Z= 0.249 Chirality : 0.041 0.145 2031 Planarity : 0.003 0.047 2448 Dihedral : 3.763 23.787 1875 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.04 % Allowed : 13.70 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1687 helix: 2.44 (0.24), residues: 462 sheet: 0.13 (0.24), residues: 462 loop : -0.42 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 348 HIS 0.002 0.001 HIS B 347 PHE 0.011 0.001 PHE A 517 TYR 0.015 0.001 TYR D 184 ARG 0.005 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 613) hydrogen bonds : angle 4.62813 ( 1755) SS BOND : bond 0.00417 ( 1) SS BOND : angle 1.93916 ( 2) covalent geometry : bond 0.00254 (13677) covalent geometry : angle 0.47386 (18569) Misc. bond : bond 0.00105 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8382 (t80) cc_final: 0.8032 (t80) REVERT: A 192 GLU cc_start: 0.8738 (tp30) cc_final: 0.8326 (tp30) REVERT: A 441 GLN cc_start: 0.8606 (tt0) cc_final: 0.8259 (tm-30) REVERT: B 311 ASP cc_start: 0.9376 (m-30) cc_final: 0.9061 (t0) REVERT: E 83 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7193 (p90) outliers start: 15 outliers final: 9 residues processed: 138 average time/residue: 2.4647 time to fit residues: 377.0544 Evaluate side-chains 131 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 83 HIS Chi-restraints excluded: chain F residue 137 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 106 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.069093 restraints weight = 66587.297| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.78 r_work: 0.2766 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13680 Z= 0.229 Angle : 0.505 6.298 18571 Z= 0.268 Chirality : 0.042 0.147 2031 Planarity : 0.003 0.051 2448 Dihedral : 3.913 25.801 1875 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.67 % Allowed : 13.91 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1687 helix: 2.33 (0.24), residues: 461 sheet: 0.01 (0.24), residues: 462 loop : -0.48 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 776 HIS 0.002 0.001 HIS D 139 PHE 0.013 0.001 PHE A 517 TYR 0.014 0.001 TYR D 184 ARG 0.007 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 613) hydrogen bonds : angle 4.66039 ( 1755) SS BOND : bond 0.00199 ( 1) SS BOND : angle 1.82053 ( 2) covalent geometry : bond 0.00520 (13677) covalent geometry : angle 0.50469 (18569) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7562 (ptp90) REVERT: A 192 GLU cc_start: 0.8795 (tp30) cc_final: 0.8385 (tp30) REVERT: A 441 GLN cc_start: 0.8666 (tt0) cc_final: 0.8351 (tm-30) REVERT: B 311 ASP cc_start: 0.9364 (m-30) cc_final: 0.9067 (t0) REVERT: E 83 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7237 (p90) outliers start: 24 outliers final: 12 residues processed: 144 average time/residue: 2.4818 time to fit residues: 395.2992 Evaluate side-chains 138 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 83 HIS Chi-restraints excluded: chain F residue 137 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 93 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.101166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.068741 restraints weight = 66846.867| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.79 r_work: 0.2748 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13680 Z= 0.200 Angle : 0.509 7.706 18571 Z= 0.267 Chirality : 0.042 0.155 2031 Planarity : 0.003 0.055 2448 Dihedral : 3.947 25.873 1875 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.39 % Allowed : 14.67 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1687 helix: 2.30 (0.24), residues: 461 sheet: 0.03 (0.24), residues: 458 loop : -0.51 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.002 0.001 HIS D 139 PHE 0.012 0.001 PHE A 517 TYR 0.014 0.001 TYR D 184 ARG 0.007 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 613) hydrogen bonds : angle 4.60512 ( 1755) SS BOND : bond 0.00191 ( 1) SS BOND : angle 1.56694 ( 2) covalent geometry : bond 0.00456 (13677) covalent geometry : angle 0.50848 (18569) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7533 (ptp90) REVERT: A 192 GLU cc_start: 0.8788 (tp30) cc_final: 0.8365 (tp30) REVERT: A 294 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: A 441 GLN cc_start: 0.8643 (tt0) cc_final: 0.8292 (tm-30) REVERT: B 311 ASP cc_start: 0.9376 (m-30) cc_final: 0.9075 (t0) REVERT: E 83 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7296 (p90) outliers start: 20 outliers final: 11 residues processed: 140 average time/residue: 2.4246 time to fit residues: 375.4921 Evaluate side-chains 139 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 83 HIS Chi-restraints excluded: chain F residue 137 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 128 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 146 optimal weight: 0.0570 chunk 98 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN F 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.101775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.069367 restraints weight = 66231.901| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.78 r_work: 0.2753 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13680 Z= 0.169 Angle : 0.495 7.650 18571 Z= 0.259 Chirality : 0.042 0.141 2031 Planarity : 0.003 0.060 2448 Dihedral : 3.917 25.219 1875 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.53 % Allowed : 14.81 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1687 helix: 2.38 (0.24), residues: 461 sheet: 0.00 (0.24), residues: 455 loop : -0.48 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 348 HIS 0.002 0.001 HIS D 139 PHE 0.011 0.001 PHE A 517 TYR 0.015 0.001 TYR D 184 ARG 0.009 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 613) hydrogen bonds : angle 4.51997 ( 1755) SS BOND : bond 0.00187 ( 1) SS BOND : angle 1.36413 ( 2) covalent geometry : bond 0.00384 (13677) covalent geometry : angle 0.49471 (18569) Misc. bond : bond 0.00080 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8811 (tp30) cc_final: 0.8380 (tp30) REVERT: A 441 GLN cc_start: 0.8664 (tt0) cc_final: 0.8322 (tm-30) REVERT: B 311 ASP cc_start: 0.9373 (m-30) cc_final: 0.9065 (t0) REVERT: E 83 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7270 (p90) REVERT: F 128 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6588 (t80) outliers start: 22 outliers final: 13 residues processed: 144 average time/residue: 2.4099 time to fit residues: 384.8662 Evaluate side-chains 139 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 83 HIS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 137 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 33 optimal weight: 0.0010 chunk 102 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.101421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.069923 restraints weight = 66596.809| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.72 r_work: 0.2764 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13680 Z= 0.152 Angle : 0.498 8.697 18571 Z= 0.259 Chirality : 0.042 0.140 2031 Planarity : 0.003 0.063 2448 Dihedral : 3.885 24.635 1875 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.32 % Allowed : 15.65 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1687 helix: 2.41 (0.24), residues: 461 sheet: -0.02 (0.24), residues: 457 loop : -0.43 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.002 0.000 HIS D 139 PHE 0.010 0.001 PHE A 517 TYR 0.015 0.001 TYR D 184 ARG 0.007 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 613) hydrogen bonds : angle 4.46586 ( 1755) SS BOND : bond 0.00156 ( 1) SS BOND : angle 1.23113 ( 2) covalent geometry : bond 0.00346 (13677) covalent geometry : angle 0.49784 (18569) Misc. bond : bond 0.00085 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8810 (tp30) cc_final: 0.8370 (tp30) REVERT: A 441 GLN cc_start: 0.8648 (tt0) cc_final: 0.8304 (tm-30) REVERT: B 311 ASP cc_start: 0.9375 (m-30) cc_final: 0.9068 (t0) REVERT: C 49 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8122 (mm-30) REVERT: E 83 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7326 (p90) REVERT: F 128 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6605 (t80) outliers start: 19 outliers final: 13 residues processed: 139 average time/residue: 2.3767 time to fit residues: 366.6062 Evaluate side-chains 138 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 83 HIS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain F residue 137 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 118 optimal weight: 0.0670 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.102392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.070179 restraints weight = 66240.250| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.80 r_work: 0.2778 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13680 Z= 0.114 Angle : 0.488 10.051 18571 Z= 0.252 Chirality : 0.041 0.138 2031 Planarity : 0.003 0.064 2448 Dihedral : 3.816 23.015 1875 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.32 % Allowed : 15.51 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1687 helix: 2.52 (0.24), residues: 461 sheet: -0.00 (0.24), residues: 457 loop : -0.38 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 348 HIS 0.004 0.001 HIS A 677 PHE 0.010 0.001 PHE A 31 TYR 0.016 0.001 TYR D 184 ARG 0.010 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 613) hydrogen bonds : angle 4.37303 ( 1755) SS BOND : bond 0.00167 ( 1) SS BOND : angle 1.14428 ( 2) covalent geometry : bond 0.00260 (13677) covalent geometry : angle 0.48832 (18569) Misc. bond : bond 0.00109 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8395 (tppt) cc_final: 0.8167 (tptm) REVERT: A 192 GLU cc_start: 0.8805 (tp30) cc_final: 0.8365 (tp30) REVERT: A 441 GLN cc_start: 0.8633 (tt0) cc_final: 0.8287 (tm-30) REVERT: A 741 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7640 (mpp) REVERT: B 311 ASP cc_start: 0.9382 (m-30) cc_final: 0.9076 (t0) REVERT: C 49 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8116 (mm-30) REVERT: E 83 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.7224 (p90) outliers start: 19 outliers final: 11 residues processed: 141 average time/residue: 2.3312 time to fit residues: 365.3023 Evaluate side-chains 141 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 83 HIS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 137 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 26 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.100857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.068560 restraints weight = 66619.744| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.78 r_work: 0.2752 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13680 Z= 0.200 Angle : 0.520 9.564 18571 Z= 0.268 Chirality : 0.042 0.143 2031 Planarity : 0.004 0.068 2448 Dihedral : 3.885 24.361 1875 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.11 % Allowed : 15.92 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1687 helix: 2.36 (0.24), residues: 460 sheet: -0.03 (0.24), residues: 457 loop : -0.44 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 776 HIS 0.002 0.001 HIS D 139 PHE 0.011 0.001 PHE A 31 TYR 0.015 0.001 TYR D 184 ARG 0.010 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 613) hydrogen bonds : angle 4.47031 ( 1755) SS BOND : bond 0.00150 ( 1) SS BOND : angle 1.22435 ( 2) covalent geometry : bond 0.00459 (13677) covalent geometry : angle 0.51950 (18569) Misc. bond : bond 0.00068 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8814 (tp30) cc_final: 0.8381 (tp30) REVERT: A 441 GLN cc_start: 0.8664 (tt0) cc_final: 0.8376 (tm-30) REVERT: A 741 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7689 (mpp) REVERT: B 311 ASP cc_start: 0.9381 (m-30) cc_final: 0.9085 (t0) REVERT: C 49 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8113 (mm-30) REVERT: E 83 HIS cc_start: 0.7826 (OUTLIER) cc_final: 0.7266 (p90) outliers start: 16 outliers final: 10 residues processed: 137 average time/residue: 2.3316 time to fit residues: 354.4218 Evaluate side-chains 132 residues out of total 1438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 83 HIS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 137 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 31 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.070245 restraints weight = 66008.505| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.77 r_work: 0.2778 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13680 Z= 0.114 Angle : 0.500 9.653 18571 Z= 0.256 Chirality : 0.041 0.138 2031 Planarity : 0.004 0.069 2448 Dihedral : 3.815 22.985 1875 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.90 % Allowed : 16.48 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1687 helix: 2.49 (0.24), residues: 460 sheet: -0.01 (0.24), residues: 457 loop : -0.37 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 348 HIS 0.002 0.000 HIS B 324 PHE 0.013 0.001 PHE A 31 TYR 0.017 0.001 TYR D 184 ARG 0.011 0.000 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 613) hydrogen bonds : angle 4.35490 ( 1755) SS BOND : bond 0.00201 ( 1) SS BOND : angle 1.12397 ( 2) covalent geometry : bond 0.00261 (13677) covalent geometry : angle 0.50008 (18569) Misc. bond : bond 0.00107 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18464.75 seconds wall clock time: 316 minutes 3.91 seconds (18963.91 seconds total)