Starting phenix.real_space_refine on Thu Jul 2 23:41:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kct_37109/07_2026/8kct_37109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kct_37109/07_2026/8kct_37109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kct_37109/07_2026/8kct_37109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kct_37109/07_2026/8kct_37109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kct_37109/07_2026/8kct_37109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kct_37109/07_2026/8kct_37109.map" } resolution = 2.6 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= 0.000 sd= 0.002 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 P 2 5.49 5 S 40 5.16 5 C 7111 2.51 5 N 1710 2.21 5 O 1974 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10839 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2436 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'O6U': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Time building chain proxies: 2.69, per 1000 atoms: 0.25 Number of scatterers: 10839 At special positions: 0 Unit cell: (109.332, 95.26, 132.065, 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 40 16.00 P 2 15.00 F 2 9.00 O 1974 8.00 N 1710 7.00 C 7111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " 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=1, symmetry=0 Links applied BETA1-3 " BMA F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 374.6 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2470 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 58.6% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 79 through 87 removed outlier: 4.052A pdb=" N GLN A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.948A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.597A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.888A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.613A pdb=" N SER A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.767A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.072A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.555A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.698A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.724A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 589 through 592 Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.751A pdb=" N GLU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.775A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 14 through 25 Processing helix chain 'C' and resid 28 through 61 removed outlier: 3.905A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 103 removed outlier: 3.738A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 140 removed outlier: 3.535A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.769A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.871A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.662A pdb=" N ALA C 212 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.791A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.592A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 81 removed outlier: 4.131A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'B' and resid 82 through 104 Proline residue: B 88 - end of helix removed outlier: 4.126A pdb=" N SER B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 156 removed outlier: 3.519A pdb=" N ARG B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 190 removed outlier: 3.550A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.713A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.834A pdb=" N ARG B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 Processing helix chain 'B' and resid 404 through 429 removed outlier: 3.641A pdb=" N ILE B 408 " --> pdb=" O TRP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 4.352A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 4.440A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.765A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL A 76 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A 94 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY A 120 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.548A pdb=" N MET A 378 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 275 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL A 363 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU A 365 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA A 279 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.508A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 93 through 95 removed outlier: 6.579A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 571 hydrogen bonds defined for protein. 1656 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: 1.70 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1633 1.31 - 1.43: 3139 1.43 - 1.56: 6275 1.56 - 1.68: 11 1.68 - 1.81: 61 Bond restraints: 11119 Sorted by residual: bond pdb=" C33 O6U B 502 " pdb=" C34 O6U B 502 " ideal model delta sigma weight residual 1.394 1.554 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C25 O6U B 502 " pdb=" C34 O6U B 502 " ideal model delta sigma weight residual 1.397 1.541 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C23 O6U B 502 " pdb=" C33 O6U B 502 " ideal model delta sigma weight residual 1.399 1.539 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C16 O6U B 502 " pdb=" C25 O6U B 502 " ideal model delta sigma weight residual 1.399 1.529 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C13 O6U B 502 " pdb=" C23 O6U B 502 " ideal model delta sigma weight residual 1.399 1.529 -0.130 2.00e-02 2.50e+03 4.21e+01 ... (remaining 11114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.72: 15134 5.72 - 11.44: 34 11.44 - 17.17: 1 17.17 - 22.89: 0 22.89 - 28.61: 1 Bond angle restraints: 15170 Sorted by residual: angle pdb=" N GLY C 233 " pdb=" CA GLY C 233 " pdb=" C GLY C 233 " ideal model delta sigma weight residual 115.43 144.04 -28.61 1.41e+00 5.03e-01 4.12e+02 angle pdb=" N GLY C 234 " pdb=" CA GLY C 234 " pdb=" C GLY C 234 " ideal model delta sigma weight residual 110.90 101.01 9.89 1.53e+00 4.27e-01 4.17e+01 angle pdb=" N ARG A 371 " pdb=" CA ARG A 371 " pdb=" C ARG A 371 " ideal model delta sigma weight residual 111.52 119.13 -7.61 1.40e+00 5.10e-01 2.95e+01 angle pdb=" N SER A 226 " pdb=" CA SER A 226 " pdb=" CB SER A 226 " ideal model delta sigma weight residual 111.56 119.47 -7.91 1.52e+00 4.33e-01 2.70e+01 angle pdb=" N LEU C 206 " pdb=" CA LEU C 206 " pdb=" C LEU C 206 " ideal model delta sigma weight residual 112.59 107.87 4.72 1.22e+00 6.72e-01 1.50e+01 ... (remaining 15165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 6625 23.50 - 47.00: 227 47.00 - 70.50: 47 70.50 - 94.01: 23 94.01 - 117.51: 18 Dihedral angle restraints: 6940 sinusoidal: 3107 harmonic: 3833 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -164.69 78.69 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" CA ASN A 91 " pdb=" C ASN A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta harmonic sigma weight residual 180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA HIS C 58 " pdb=" C HIS C 58 " pdb=" N VAL C 59 " pdb=" CA VAL C 59 " ideal model delta harmonic sigma weight residual 180.00 152.75 27.25 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 6937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1699 0.101 - 0.202: 99 0.202 - 0.302: 6 0.302 - 0.403: 5 0.403 - 0.504: 1 Chirality restraints: 1810 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA SER A 226 " pdb=" N SER A 226 " pdb=" C SER A 226 " pdb=" CB SER A 226 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 1807 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.025 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP C 227 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " -0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 243 " -0.058 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO A 244 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 244 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 244 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO A 560 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.040 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 87 2.59 - 3.17: 8962 3.17 - 3.75: 16513 3.75 - 4.32: 23142 4.32 - 4.90: 38058 Nonbonded interactions: 86762 Sorted by model distance: nonbonded pdb=" O MET B 233 " pdb=" CD2 PHE B 237 " model vdw 2.017 3.340 nonbonded pdb=" O ALA B 98 " pdb=" OG SER B 102 " model vdw 2.181 3.040 nonbonded pdb=" OH TYR D 18 " pdb=" O LYS B 216 " model vdw 2.194 3.040 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.214 3.040 nonbonded pdb=" CE MET B 233 " pdb=" CZ PHE B 237 " model vdw 2.251 3.760 ... (remaining 86757 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 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.450 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 0.160 11145 Z= 0.362 Angle : 0.947 28.612 15241 Z= 0.498 Chirality : 0.058 0.504 1810 Planarity : 0.007 0.087 1829 Dihedral : 14.712 117.506 4458 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.89 % Allowed : 4.26 % Favored : 94.85 % Cbeta Deviations : 0.08 % 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 are not related in a simple way. whole: -3.09 (0.19), residues: 1303 helix: -1.44 (0.16), residues: 713 sheet: -1.54 (0.47), residues: 114 loop : -3.00 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 626 TYR 0.035 0.002 TYR A 565 PHE 0.036 0.002 PHE C 132 TRP 0.053 0.003 TRP C 227 HIS 0.024 0.003 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00764 / 0.36 (11119) covalent geometry : angle 0.91861 / 0.49 (15170) SS BOND : bond 0.00734 / 0.37 ( 4) SS BOND : angle 2.41575 / 1.34 ( 8) hydrogen bonds : bond 0.18437 / 12.68 ( 571) hydrogen bonds : angle 6.79104 / 4.52 ( 1656) Misc. bond : bond 0.00925 / 0.49 ( 1) link_BETA1-3 : bond 0.00096 / 0.05 ( 1) link_BETA1-3 : angle 1.61103 / 1.18 ( 3) link_BETA1-4 : bond 0.00174 / 0.09 ( 7) link_BETA1-4 : angle 2.20629 / 1.59 ( 21) link_BETA1-6 : bond 0.00534 / 0.28 ( 1) link_BETA1-6 : angle 1.47795 / 1.26 ( 3) link_NAG-ASN : bond 0.01011 / 0.56 ( 12) link_NAG-ASN : angle 4.45339 / 3.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: C 68 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8488 (mm110) REVERT: C 95 LYS cc_start: 0.8200 (tptm) cc_final: 0.7873 (tptp) REVERT: C 180 ASP cc_start: 0.8760 (t70) cc_final: 0.7752 (t0) REVERT: C 183 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7958 (tp30) REVERT: D 40 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8233 (mp0) REVERT: D 49 GLU cc_start: 0.8366 (mp0) cc_final: 0.7786 (pm20) REVERT: B 84 MET cc_start: 0.9117 (mtt) cc_final: 0.8810 (mtp) REVERT: B 146 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6514 (mmm) outliers start: 10 outliers final: 3 residues processed: 155 average time/residue: 0.6431 time to fit residues: 106.8266 Evaluate side-chains 80 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 HIS A 142 ASN A 355 GLN A 358 ASN A 444 HIS A 454 GLN A 531 ASN A 606 GLN C 68 GLN D 52 GLN B 279 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.061489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.046792 restraints weight = 30439.302| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.74 r_work: 0.2584 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 11145 Z= 0.273 Angle : 0.771 10.659 15241 Z= 0.378 Chirality : 0.048 0.245 1810 Planarity : 0.005 0.047 1829 Dihedral : 11.665 108.390 2158 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.31 % Allowed : 9.33 % Favored : 88.37 % 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 are not related in a simple way. whole: -0.86 (0.22), residues: 1303 helix: 0.69 (0.19), residues: 707 sheet: -0.97 (0.52), residues: 98 loop : -2.37 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 377 TYR 0.021 0.002 TYR A 173 PHE 0.038 0.003 PHE A 302 TRP 0.025 0.002 TRP C 209 HIS 0.012 0.002 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.27 (11119) covalent geometry : angle 0.74507 / 0.37 (15170) SS BOND : bond 0.00680 / 0.34 ( 4) SS BOND : angle 1.33390 / 0.65 ( 8) hydrogen bonds : bond 0.05389 / 3.61 ( 571) hydrogen bonds : angle 4.31090 / 2.90 ( 1656) Misc. bond : bond 0.00244 / 0.13 ( 1) link_BETA1-3 : bond 0.00684 / 0.36 ( 1) link_BETA1-3 : angle 2.47379 / 1.75 ( 3) link_BETA1-4 : bond 0.00134 / 0.06 ( 7) link_BETA1-4 : angle 2.05413 / 1.37 ( 21) link_BETA1-6 : bond 0.01596 / 0.84 ( 1) link_BETA1-6 : angle 4.04049 / 2.96 ( 3) link_NAG-ASN : bond 0.00571 / 0.28 ( 12) link_NAG-ASN : angle 3.64813 / 2.59 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.336 Fit side-chains REVERT: A 240 PHE cc_start: 0.7956 (m-80) cc_final: 0.7649 (m-10) REVERT: C 180 ASP cc_start: 0.9000 (t70) cc_final: 0.8404 (t0) REVERT: C 183 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8427 (mm-30) REVERT: D 40 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8700 (mp0) REVERT: D 49 GLU cc_start: 0.8585 (mp0) cc_final: 0.8275 (mp0) REVERT: B 84 MET cc_start: 0.9256 (mtt) cc_final: 0.8994 (mtp) REVERT: B 146 MET cc_start: 0.6845 (ptm) cc_final: 0.6389 (mmm) REVERT: B 403 ASP cc_start: 0.8547 (p0) cc_final: 0.8316 (p0) REVERT: B 454 GLN cc_start: 0.9171 (tp40) cc_final: 0.8943 (tp40) outliers start: 26 outliers final: 8 residues processed: 95 average time/residue: 0.5696 time to fit residues: 58.5130 Evaluate side-chains 74 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.060694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.046001 restraints weight = 30760.953| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.72 r_work: 0.2560 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11145 Z= 0.246 Angle : 0.695 10.705 15241 Z= 0.343 Chirality : 0.046 0.227 1810 Planarity : 0.004 0.037 1829 Dihedral : 10.349 109.076 2151 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.95 % Allowed : 11.63 % Favored : 86.41 % 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 are not related in a simple way. whole: -0.11 (0.23), residues: 1303 helix: 1.33 (0.19), residues: 716 sheet: -0.89 (0.50), residues: 112 loop : -2.12 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 87 TYR 0.018 0.002 TYR C 218 PHE 0.030 0.002 PHE A 302 TRP 0.017 0.002 TRP D 36 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (11119) covalent geometry : angle 0.67357 / 0.34 (15170) SS BOND : bond 0.00602 / 0.30 ( 4) SS BOND : angle 1.51270 / 0.73 ( 8) hydrogen bonds : bond 0.05085 / 3.45 ( 571) hydrogen bonds : angle 4.07893 / 2.73 ( 1656) Misc. bond : bond 0.00178 / 0.09 ( 1) link_BETA1-3 : bond 0.00504 / 0.27 ( 1) link_BETA1-3 : angle 1.69506 / 1.18 ( 3) link_BETA1-4 : bond 0.00206 / 0.10 ( 7) link_BETA1-4 : angle 1.96494 / 1.28 ( 21) link_BETA1-6 : bond 0.01488 / 0.78 ( 1) link_BETA1-6 : angle 3.08028 / 2.49 ( 3) link_NAG-ASN : bond 0.00500 / 0.24 ( 12) link_NAG-ASN : angle 3.13077 / 2.42 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 364 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8830 (tt0) REVERT: A 481 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9113 (p) REVERT: C 106 GLU cc_start: 0.7331 (tp30) cc_final: 0.6919 (tp30) REVERT: C 180 ASP cc_start: 0.8981 (t70) cc_final: 0.8378 (t0) REVERT: D 13 ASN cc_start: 0.8318 (m110) cc_final: 0.7919 (t0) REVERT: D 40 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8564 (mp0) REVERT: D 49 GLU cc_start: 0.8682 (mp0) cc_final: 0.8278 (mp0) REVERT: B 84 MET cc_start: 0.9232 (mtt) cc_final: 0.8952 (mtp) REVERT: B 257 ASP cc_start: 0.9140 (t0) cc_final: 0.8901 (t0) REVERT: B 403 ASP cc_start: 0.8418 (p0) cc_final: 0.8144 (p0) REVERT: B 454 GLN cc_start: 0.9167 (tp40) cc_final: 0.8946 (tp40) outliers start: 22 outliers final: 7 residues processed: 90 average time/residue: 0.6132 time to fit residues: 59.6021 Evaluate side-chains 74 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 0.0170 chunk 71 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 385 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.063147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.048524 restraints weight = 30448.504| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.74 r_work: 0.2626 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11145 Z= 0.116 Angle : 0.582 10.527 15241 Z= 0.284 Chirality : 0.042 0.247 1810 Planarity : 0.004 0.035 1829 Dihedral : 9.457 101.564 2149 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.69 % Allowed : 12.70 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1303 helix: 1.91 (0.19), residues: 713 sheet: -0.54 (0.52), residues: 106 loop : -1.85 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 432 TYR 0.015 0.001 TYR B 256 PHE 0.029 0.001 PHE A 302 TRP 0.009 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (11119) covalent geometry : angle 0.56523 / 0.28 (15170) SS BOND : bond 0.00328 / 0.16 ( 4) SS BOND : angle 1.11582 / 0.59 ( 8) hydrogen bonds : bond 0.03786 / 2.57 ( 571) hydrogen bonds : angle 3.78035 / 2.53 ( 1656) Misc. bond : bond 0.00174 / 0.09 ( 1) link_BETA1-3 : bond 0.00899 / 0.47 ( 1) link_BETA1-3 : angle 1.78713 / 1.11 ( 3) link_BETA1-4 : bond 0.00339 / 0.17 ( 7) link_BETA1-4 : angle 1.59985 / 1.05 ( 21) link_BETA1-6 : bond 0.01537 / 0.81 ( 1) link_BETA1-6 : angle 3.49960 / 3.05 ( 3) link_NAG-ASN : bond 0.00389 / 0.20 ( 12) link_NAG-ASN : angle 2.44142 / 1.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: C 69 TYR cc_start: 0.8755 (t80) cc_final: 0.8409 (t80) REVERT: C 106 GLU cc_start: 0.7376 (tp30) cc_final: 0.6911 (tp30) REVERT: C 180 ASP cc_start: 0.8904 (t70) cc_final: 0.8357 (t0) REVERT: D 49 GLU cc_start: 0.8613 (mp0) cc_final: 0.8162 (mp0) REVERT: D 84 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8418 (mtp180) REVERT: B 84 MET cc_start: 0.9148 (mtt) cc_final: 0.8882 (mtp) REVERT: B 257 ASP cc_start: 0.9106 (t0) cc_final: 0.8814 (t0) REVERT: B 403 ASP cc_start: 0.8257 (p0) cc_final: 0.7936 (p0) outliers start: 19 outliers final: 7 residues processed: 90 average time/residue: 0.5566 time to fit residues: 54.6239 Evaluate side-chains 71 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 0.0970 chunk 41 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.060105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.045402 restraints weight = 30475.923| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.70 r_work: 0.2540 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 11145 Z= 0.281 Angle : 0.693 11.503 15241 Z= 0.338 Chirality : 0.046 0.230 1810 Planarity : 0.004 0.040 1829 Dihedral : 9.576 82.796 2149 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.31 % Allowed : 12.70 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.24), residues: 1303 helix: 2.08 (0.19), residues: 705 sheet: -0.71 (0.50), residues: 112 loop : -1.71 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 626 TYR 0.016 0.002 TYR B 189 PHE 0.027 0.002 PHE A 302 TRP 0.017 0.001 TRP C 209 HIS 0.008 0.002 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.28 (11119) covalent geometry : angle 0.67203 / 0.33 (15170) SS BOND : bond 0.00625 / 0.31 ( 4) SS BOND : angle 1.52717 / 0.74 ( 8) hydrogen bonds : bond 0.04737 / 3.21 ( 571) hydrogen bonds : angle 3.88203 / 2.59 ( 1656) Misc. bond : bond 0.00187 / 0.10 ( 1) link_BETA1-3 : bond 0.00554 / 0.29 ( 1) link_BETA1-3 : angle 1.89278 / 1.25 ( 3) link_BETA1-4 : bond 0.00195 / 0.10 ( 7) link_BETA1-4 : angle 1.89550 / 1.21 ( 21) link_BETA1-6 : bond 0.01232 / 0.65 ( 1) link_BETA1-6 : angle 3.39540 / 2.76 ( 3) link_NAG-ASN : bond 0.00536 / 0.25 ( 12) link_NAG-ASN : angle 3.01943 / 2.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: C 99 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: C 106 GLU cc_start: 0.7445 (tp30) cc_final: 0.6946 (tp30) REVERT: C 180 ASP cc_start: 0.9014 (t70) cc_final: 0.8423 (t0) REVERT: C 211 GLU cc_start: 0.8948 (pt0) cc_final: 0.8356 (pm20) REVERT: D 40 GLU cc_start: 0.8577 (mp0) cc_final: 0.8314 (mm-30) REVERT: D 49 GLU cc_start: 0.8847 (mp0) cc_final: 0.8401 (mp0) REVERT: B 84 MET cc_start: 0.9247 (mtt) cc_final: 0.8973 (mtp) REVERT: B 257 ASP cc_start: 0.9205 (t0) cc_final: 0.8888 (t0) REVERT: B 403 ASP cc_start: 0.8468 (p0) cc_final: 0.8168 (p0) REVERT: B 454 GLN cc_start: 0.9157 (tp40) cc_final: 0.8852 (tp40) outliers start: 26 outliers final: 12 residues processed: 88 average time/residue: 0.5453 time to fit residues: 52.0143 Evaluate side-chains 74 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.047064 restraints weight = 30809.072| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.67 r_work: 0.2592 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11145 Z= 0.146 Angle : 0.612 11.412 15241 Z= 0.297 Chirality : 0.043 0.232 1810 Planarity : 0.004 0.036 1829 Dihedral : 9.030 79.877 2149 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.22 % Allowed : 13.23 % Favored : 84.55 % 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 are not related in a simple way. whole: 1.01 (0.24), residues: 1303 helix: 2.30 (0.20), residues: 704 sheet: -0.67 (0.48), residues: 120 loop : -1.54 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 626 TYR 0.014 0.001 TYR A 569 PHE 0.028 0.001 PHE A 302 TRP 0.010 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (11119) covalent geometry : angle 0.59405 / 0.29 (15170) SS BOND : bond 0.00417 / 0.21 ( 4) SS BOND : angle 1.34223 / 0.71 ( 8) hydrogen bonds : bond 0.04016 / 2.73 ( 571) hydrogen bonds : angle 3.75689 / 2.51 ( 1656) Misc. bond : bond 0.00186 / 0.10 ( 1) link_BETA1-3 : bond 0.00533 / 0.28 ( 1) link_BETA1-3 : angle 1.67075 / 1.07 ( 3) link_BETA1-4 : bond 0.00249 / 0.12 ( 7) link_BETA1-4 : angle 1.62103 / 1.05 ( 21) link_BETA1-6 : bond 0.00981 / 0.52 ( 1) link_BETA1-6 : angle 3.20509 / 2.43 ( 3) link_NAG-ASN : bond 0.00393 / 0.18 ( 12) link_NAG-ASN : angle 2.62898 / 2.12 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 481 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9067 (p) REVERT: C 106 GLU cc_start: 0.7422 (tp30) cc_final: 0.6923 (tp30) REVERT: C 180 ASP cc_start: 0.9065 (t70) cc_final: 0.8516 (t0) REVERT: C 211 GLU cc_start: 0.8982 (pt0) cc_final: 0.8397 (pm20) REVERT: D 40 GLU cc_start: 0.8622 (mp0) cc_final: 0.8369 (mm-30) REVERT: D 49 GLU cc_start: 0.8799 (mp0) cc_final: 0.8232 (mp0) REVERT: B 84 MET cc_start: 0.9218 (mtt) cc_final: 0.8951 (mtp) REVERT: B 257 ASP cc_start: 0.9189 (t0) cc_final: 0.8864 (t0) REVERT: B 403 ASP cc_start: 0.8411 (p0) cc_final: 0.8062 (p0) REVERT: B 454 GLN cc_start: 0.9146 (tp40) cc_final: 0.8912 (tp40) outliers start: 25 outliers final: 9 residues processed: 88 average time/residue: 0.5118 time to fit residues: 49.1988 Evaluate side-chains 74 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.061454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.046952 restraints weight = 30887.748| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.68 r_work: 0.2587 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11145 Z= 0.150 Angle : 0.607 11.449 15241 Z= 0.293 Chirality : 0.042 0.230 1810 Planarity : 0.004 0.037 1829 Dihedral : 8.694 80.336 2149 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 1.87 % Allowed : 13.41 % Favored : 84.72 % 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 are not related in a simple way. whole: 1.10 (0.24), residues: 1303 helix: 2.36 (0.19), residues: 706 sheet: -0.79 (0.47), residues: 124 loop : -1.44 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 87 TYR 0.013 0.001 TYR A 569 PHE 0.027 0.001 PHE A 302 TRP 0.011 0.001 TRP C 209 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (11119) covalent geometry : angle 0.58963 / 0.29 (15170) SS BOND : bond 0.00428 / 0.21 ( 4) SS BOND : angle 1.33949 / 0.70 ( 8) hydrogen bonds : bond 0.03943 / 2.68 ( 571) hydrogen bonds : angle 3.71465 / 2.48 ( 1656) Misc. bond : bond 0.00189 / 0.10 ( 1) link_BETA1-3 : bond 0.00628 / 0.33 ( 1) link_BETA1-3 : angle 1.47828 / 1.04 ( 3) link_BETA1-4 : bond 0.00193 / 0.09 ( 7) link_BETA1-4 : angle 1.59863 / 1.03 ( 21) link_BETA1-6 : bond 0.00874 / 0.46 ( 1) link_BETA1-6 : angle 2.92924 / 2.16 ( 3) link_NAG-ASN : bond 0.00366 / 0.17 ( 12) link_NAG-ASN : angle 2.57070 / 2.08 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 481 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9060 (p) REVERT: C 96 LYS cc_start: 0.7580 (ttpt) cc_final: 0.6755 (tppp) REVERT: C 106 GLU cc_start: 0.7442 (tp30) cc_final: 0.6930 (tp30) REVERT: C 180 ASP cc_start: 0.9100 (t70) cc_final: 0.8560 (t0) REVERT: C 211 GLU cc_start: 0.8962 (pt0) cc_final: 0.8410 (pm20) REVERT: D 40 GLU cc_start: 0.8710 (mp0) cc_final: 0.8499 (mt-10) REVERT: D 49 GLU cc_start: 0.8473 (mp0) cc_final: 0.8162 (mp0) REVERT: B 84 MET cc_start: 0.9219 (mtt) cc_final: 0.8952 (mtp) REVERT: B 257 ASP cc_start: 0.9199 (t0) cc_final: 0.8869 (t0) REVERT: B 403 ASP cc_start: 0.8420 (p0) cc_final: 0.8077 (p0) outliers start: 21 outliers final: 11 residues processed: 82 average time/residue: 0.5406 time to fit residues: 48.2205 Evaluate side-chains 73 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 75 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 chunk 65 optimal weight: 0.0070 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 GLN B 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.062971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.048549 restraints weight = 30714.554| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.68 r_work: 0.2628 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11145 Z= 0.108 Angle : 0.577 11.053 15241 Z= 0.278 Chirality : 0.041 0.238 1810 Planarity : 0.003 0.036 1829 Dihedral : 8.252 82.814 2149 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 1.51 % Allowed : 13.94 % Favored : 84.55 % 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 are not related in a simple way. whole: 1.30 (0.24), residues: 1303 helix: 2.49 (0.19), residues: 706 sheet: -0.67 (0.48), residues: 124 loop : -1.31 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 108 TYR 0.012 0.001 TYR A 569 PHE 0.028 0.001 PHE A 302 TRP 0.008 0.001 TRP D 58 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (11119) covalent geometry : angle 0.56252 / 0.27 (15170) SS BOND : bond 0.00304 / 0.15 ( 4) SS BOND : angle 1.18142 / 0.66 ( 8) hydrogen bonds : bond 0.03448 / 2.36 ( 571) hydrogen bonds : angle 3.64344 / 2.43 ( 1656) Misc. bond : bond 0.00178 / 0.09 ( 1) link_BETA1-3 : bond 0.00723 / 0.38 ( 1) link_BETA1-3 : angle 1.38623 / 0.98 ( 3) link_BETA1-4 : bond 0.00294 / 0.15 ( 7) link_BETA1-4 : angle 1.41575 / 0.94 ( 21) link_BETA1-6 : bond 0.00863 / 0.45 ( 1) link_BETA1-6 : angle 2.66842 / 1.99 ( 3) link_NAG-ASN : bond 0.00352 / 0.17 ( 12) link_NAG-ASN : angle 2.33790 / 1.94 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 481 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.9057 (p) REVERT: C 96 LYS cc_start: 0.7546 (ttpt) cc_final: 0.6769 (tppp) REVERT: C 106 GLU cc_start: 0.7399 (tp30) cc_final: 0.6860 (tp30) REVERT: C 180 ASP cc_start: 0.9083 (t70) cc_final: 0.8560 (t0) REVERT: C 211 GLU cc_start: 0.8952 (pt0) cc_final: 0.8402 (pm20) REVERT: D 10 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7754 (pp20) REVERT: D 40 GLU cc_start: 0.8676 (mp0) cc_final: 0.8464 (mt-10) REVERT: D 49 GLU cc_start: 0.8445 (mp0) cc_final: 0.8174 (mp0) REVERT: B 84 MET cc_start: 0.9195 (mtt) cc_final: 0.8919 (mtp) REVERT: B 257 ASP cc_start: 0.9175 (t0) cc_final: 0.8831 (t0) outliers start: 17 outliers final: 6 residues processed: 81 average time/residue: 0.5617 time to fit residues: 49.6169 Evaluate side-chains 71 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.061093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.046687 restraints weight = 30845.881| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 2.66 r_work: 0.2575 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11145 Z= 0.191 Angle : 0.629 11.671 15241 Z= 0.306 Chirality : 0.043 0.228 1810 Planarity : 0.004 0.038 1829 Dihedral : 8.313 80.784 2149 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 1.33 % Allowed : 14.12 % Favored : 84.55 % 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 are not related in a simple way. whole: 1.26 (0.24), residues: 1303 helix: 2.45 (0.20), residues: 707 sheet: -0.73 (0.47), residues: 124 loop : -1.32 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.014 0.001 TYR A 569 PHE 0.026 0.001 PHE A 302 TRP 0.013 0.001 TRP C 209 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (11119) covalent geometry : angle 0.61227 / 0.30 (15170) SS BOND : bond 0.00494 / 0.25 ( 4) SS BOND : angle 1.32425 / 0.66 ( 8) hydrogen bonds : bond 0.04079 / 2.78 ( 571) hydrogen bonds : angle 3.71245 / 2.48 ( 1656) Misc. bond : bond 0.00194 / 0.10 ( 1) link_BETA1-3 : bond 0.00563 / 0.30 ( 1) link_BETA1-3 : angle 1.58844 / 1.13 ( 3) link_BETA1-4 : bond 0.00191 / 0.09 ( 7) link_BETA1-4 : angle 1.66191 / 1.07 ( 21) link_BETA1-6 : bond 0.00742 / 0.39 ( 1) link_BETA1-6 : angle 2.35110 / 1.74 ( 3) link_NAG-ASN : bond 0.00419 / 0.19 ( 12) link_NAG-ASN : angle 2.61850 / 2.08 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 481 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9075 (p) REVERT: C 96 LYS cc_start: 0.7558 (ttpt) cc_final: 0.6804 (tppp) REVERT: C 106 GLU cc_start: 0.7484 (tp30) cc_final: 0.6940 (tp30) REVERT: C 180 ASP cc_start: 0.9120 (t70) cc_final: 0.8580 (t0) REVERT: C 211 GLU cc_start: 0.9008 (pt0) cc_final: 0.8519 (pm20) REVERT: D 10 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7848 (pp20) REVERT: D 49 GLU cc_start: 0.8515 (mp0) cc_final: 0.8237 (mp0) REVERT: B 84 MET cc_start: 0.9216 (mtt) cc_final: 0.8946 (mtp) REVERT: B 257 ASP cc_start: 0.9194 (t0) cc_final: 0.8867 (t0) outliers start: 15 outliers final: 8 residues processed: 74 average time/residue: 0.6201 time to fit residues: 49.6574 Evaluate side-chains 73 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 644 GLU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 114 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.061607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.047110 restraints weight = 30600.871| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.66 r_work: 0.2593 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11145 Z= 0.149 Angle : 0.604 11.458 15241 Z= 0.292 Chirality : 0.042 0.228 1810 Planarity : 0.004 0.037 1829 Dihedral : 8.097 82.041 2149 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 0.89 % Allowed : 14.83 % Favored : 84.28 % 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 are not related in a simple way. whole: 1.27 (0.24), residues: 1303 helix: 2.41 (0.19), residues: 712 sheet: -0.74 (0.47), residues: 124 loop : -1.27 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 629 TYR 0.012 0.001 TYR A 569 PHE 0.027 0.001 PHE A 302 TRP 0.012 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (11119) covalent geometry : angle 0.58877 / 0.29 (15170) SS BOND : bond 0.00417 / 0.21 ( 4) SS BOND : angle 1.27700 / 0.67 ( 8) hydrogen bonds : bond 0.03854 / 2.63 ( 571) hydrogen bonds : angle 3.68922 / 2.46 ( 1656) Misc. bond : bond 0.00190 / 0.10 ( 1) link_BETA1-3 : bond 0.00599 / 0.32 ( 1) link_BETA1-3 : angle 1.54467 / 1.10 ( 3) link_BETA1-4 : bond 0.00232 / 0.11 ( 7) link_BETA1-4 : angle 1.55426 / 1.02 ( 21) link_BETA1-6 : bond 0.00746 / 0.39 ( 1) link_BETA1-6 : angle 1.98547 / 1.50 ( 3) link_NAG-ASN : bond 0.00386 / 0.18 ( 12) link_NAG-ASN : angle 2.49446 / 2.04 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 481 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9067 (p) REVERT: C 96 LYS cc_start: 0.7526 (ttpt) cc_final: 0.6836 (tppp) REVERT: C 106 GLU cc_start: 0.7420 (tp30) cc_final: 0.6894 (tp30) REVERT: C 180 ASP cc_start: 0.9135 (t70) cc_final: 0.8600 (t0) REVERT: C 211 GLU cc_start: 0.8998 (pt0) cc_final: 0.8511 (pm20) REVERT: B 84 MET cc_start: 0.9216 (mtt) cc_final: 0.8950 (mtp) REVERT: B 257 ASP cc_start: 0.9184 (t0) cc_final: 0.8847 (t0) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.6514 time to fit residues: 50.7174 Evaluate side-chains 68 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 39 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 0.3980 chunk 115 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.062063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.047557 restraints weight = 30915.897| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.68 r_work: 0.2605 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11145 Z= 0.132 Angle : 0.596 11.090 15241 Z= 0.290 Chirality : 0.042 0.235 1810 Planarity : 0.003 0.037 1829 Dihedral : 7.913 83.101 2149 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 0.98 % Allowed : 14.92 % Favored : 84.10 % 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 are not related in a simple way. whole: 1.34 (0.24), residues: 1303 helix: 2.46 (0.19), residues: 712 sheet: -0.68 (0.47), residues: 124 loop : -1.22 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 629 TYR 0.016 0.001 TYR D 47 PHE 0.027 0.001 PHE A 302 TRP 0.012 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (11119) covalent geometry : angle 0.58171 / 0.29 (15170) SS BOND : bond 0.00372 / 0.19 ( 4) SS BOND : angle 1.23484 / 0.65 ( 8) hydrogen bonds : bond 0.03718 / 2.54 ( 571) hydrogen bonds : angle 3.66460 / 2.44 ( 1656) Misc. bond : bond 0.00191 / 0.10 ( 1) link_BETA1-3 : bond 0.00605 / 0.32 ( 1) link_BETA1-3 : angle 1.49426 / 1.07 ( 3) link_BETA1-4 : bond 0.00200 / 0.10 ( 7) link_BETA1-4 : angle 1.51495 / 1.00 ( 21) link_BETA1-6 : bond 0.00707 / 0.37 ( 1) link_BETA1-6 : angle 1.64447 / 1.30 ( 3) link_NAG-ASN : bond 0.00366 / 0.17 ( 12) link_NAG-ASN : angle 2.38389 / 1.96 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3389.40 seconds wall clock time: 58 minutes 40.03 seconds (3520.03 seconds total)