Starting phenix.real_space_refine on Thu Jul 2 23:13:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcp_37107/07_2026/8kcp_37107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcp_37107/07_2026/8kcp_37107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kcp_37107/07_2026/8kcp_37107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcp_37107/07_2026/8kcp_37107.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kcp_37107/07_2026/8kcp_37107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcp_37107/07_2026/8kcp_37107.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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 P 2 5.49 5 S 40 5.16 5 C 7106 2.51 5 N 1709 2.21 5 O 1977 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 10837 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: "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: "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: "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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'N9C': 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 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 Time building chain proxies: 2.20, per 1000 atoms: 0.20 Number of scatterers: 10837 At special positions: 0 Unit cell: (109.332, 94.1775, 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 3 9.00 O 1977 8.00 N 1709 7.00 C 7106 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: 0.92 Conformation dependent library (CDL) restraints added in 309.0 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: 51 helices and 6 sheets defined 58.8% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 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: 4.073A 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: 3.723A 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: 3.750A 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 'B' and resid 77 through 103 removed outlier: 3.537A pdb=" N MET B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 124 through 156 Processing helix chain 'B' and resid 158 through 176 removed outlier: 3.615A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 190 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: 3.920A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.505A pdb=" N THR B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 429 removed outlier: 3.977A pdb=" N THR B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.625A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) 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: 3.952A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.577A 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: 3.846A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 103 removed outlier: 3.739A 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: 3.768A 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: 3.587A 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: 3.661A 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: 4.130A 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: 3.502A 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 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: 6.531A 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: 5.506A 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: 6.776A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N VAL A 76 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.328A 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: 6.480A 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: 9.043A 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: 6.537A 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: 6.665A 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: 3.509A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.552A 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 289 573 hydrogen bonds defined for protein. 1662 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: 1.43 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1635 1.30 - 1.43: 3099 1.43 - 1.56: 6313 1.56 - 1.68: 9 1.68 - 1.81: 61 Bond restraints: 11117 Sorted by residual: bond pdb=" C24 N9C B 502 " pdb=" C26 N9C B 502 " ideal model delta sigma weight residual 1.397 1.542 -0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" C13 N9C B 502 " pdb=" C19 N9C B 502 " ideal model delta sigma weight residual 1.398 1.539 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C28 N9C B 502 " pdb=" C29 N9C B 502 " ideal model delta sigma weight residual 1.404 1.542 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C14 N9C B 502 " pdb=" C22 N9C B 502 " ideal model delta sigma weight residual 1.403 1.540 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C22 N9C B 502 " pdb=" C26 N9C B 502 " ideal model delta sigma weight residual 1.397 1.533 -0.136 2.00e-02 2.50e+03 4.64e+01 ... (remaining 11112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.72: 15119 5.72 - 11.45: 44 11.45 - 17.17: 2 17.17 - 22.90: 0 22.90 - 28.62: 1 Bond angle restraints: 15166 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 115.43 144.05 -28.62 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 110.90 101.02 9.88 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 111.52 119.14 -7.62 1.40e+00 5.10e-01 2.96e+01 angle pdb=" N SER A 226 " pdb=" CA SER A 226 " pdb=" CB SER A 226 " ideal model delta sigma weight residual 111.56 119.49 -7.93 1.52e+00 4.33e-01 2.72e+01 angle pdb=" N VAL B 261 " pdb=" CA VAL B 261 " pdb=" C VAL B 261 " ideal model delta sigma weight residual 112.96 108.64 4.32 1.00e+00 1.00e+00 1.87e+01 ... (remaining 15161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 6666 23.50 - 47.00: 182 47.00 - 70.50: 49 70.50 - 94.00: 20 94.00 - 117.51: 18 Dihedral angle restraints: 6935 sinusoidal: 3102 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 -152.01 -27.99 0 5.00e+00 4.00e-02 3.13e+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 6932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1667 0.100 - 0.200: 132 0.200 - 0.300: 5 0.300 - 0.400: 5 0.400 - 0.500: 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 6.24e+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 -0.39 2.00e-01 2.50e+01 3.71e+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 3.32e+00 ... (remaining 1807 not shown) Planarity restraints: 1843 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 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " -0.032 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 8.03e+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 1840 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1445 2.75 - 3.29: 10284 3.29 - 3.83: 17819 3.83 - 4.36: 20782 4.36 - 4.90: 36031 Nonbonded interactions: 86361 Sorted by model distance: nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.264 3.040 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.297 3.040 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.311 3.040 nonbonded pdb=" O LEU B 174 " pdb=" OG SER B 178 " model vdw 2.318 3.040 ... (remaining 86356 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.120 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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 0.145 11143 Z= 0.404 Angle : 1.019 28.623 15237 Z= 0.535 Chirality : 0.061 0.500 1810 Planarity : 0.007 0.087 1831 Dihedral : 14.174 117.506 4453 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.44 % Allowed : 1.78 % Favored : 97.78 % 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: -3.42 (0.18), residues: 1303 helix: -1.86 (0.15), residues: 711 sheet: -1.54 (0.47), residues: 114 loop : -2.90 (0.23), residues: 478 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 0.003 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 0.00840 / 0.40 (11117) covalent geometry : angle 0.99232 / 0.53 (15166) SS BOND : bond 0.00711 / 0.35 ( 4) SS BOND : angle 2.41098 / 1.33 ( 8) hydrogen bonds : bond 0.18849 / 13.01 ( 573) hydrogen bonds : angle 7.02989 / 4.73 ( 1662) Misc. bond : bond 0.00904 / 0.48 ( 1) link_BETA1-3 : bond 0.00089 / 0.05 ( 1) link_BETA1-3 : angle 1.60126 / 1.18 ( 3) link_BETA1-4 : bond 0.00193 / 0.10 ( 7) link_BETA1-4 : angle 2.20556 / 1.58 ( 21) link_BETA1-6 : bond 0.00546 / 0.29 ( 1) link_BETA1-6 : angle 1.47199 / 1.25 ( 3) link_NAG-ASN : bond 0.01026 / 0.57 ( 12) link_NAG-ASN : angle 4.44871 / 3.47 ( 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 160 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8440 (ttm) cc_final: 0.8094 (ttp) REVERT: A 245 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8504 (mp0) REVERT: A 461 GLU cc_start: 0.8609 (mp0) cc_final: 0.8378 (mp0) REVERT: A 654 LYS cc_start: 0.9238 (ptpt) cc_final: 0.8828 (ptpp) REVERT: B 110 ASP cc_start: 0.8158 (m-30) cc_final: 0.7878 (m-30) REVERT: B 165 TRP cc_start: 0.8895 (t60) cc_final: 0.8639 (t60) REVERT: B 194 ASP cc_start: 0.9117 (p0) cc_final: 0.8149 (p0) REVERT: B 210 MET cc_start: 0.9296 (mmt) cc_final: 0.9007 (mmm) REVERT: B 257 ASP cc_start: 0.9126 (t70) cc_final: 0.8645 (t0) REVERT: B 269 ARG cc_start: 0.9141 (ttt-90) cc_final: 0.8582 (tmm-80) REVERT: B 403 ASP cc_start: 0.8796 (m-30) cc_final: 0.8511 (m-30) REVERT: B 454 GLN cc_start: 0.8408 (tp-100) cc_final: 0.7588 (tp-100) REVERT: B 458 ASP cc_start: 0.8739 (m-30) cc_final: 0.8227 (m-30) REVERT: C 140 ASP cc_start: 0.8535 (m-30) cc_final: 0.7355 (m-30) REVERT: C 180 ASP cc_start: 0.9269 (t70) cc_final: 0.8647 (t0) REVERT: C 183 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8167 (mm-30) REVERT: C 211 GLU cc_start: 0.8745 (pt0) cc_final: 0.8135 (pm20) REVERT: D 17 LYS cc_start: 0.8705 (mttm) cc_final: 0.8502 (mttm) REVERT: D 40 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8898 (OUTLIER) REVERT: D 47 TYR cc_start: 0.8600 (p90) cc_final: 0.8123 (p90) REVERT: D 54 LYS cc_start: 0.9423 (ttpt) cc_final: 0.9093 (ttpm) outliers start: 5 outliers final: 1 residues processed: 159 average time/residue: 0.5056 time to fit residues: 87.2585 Evaluate side-chains 104 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 HIS A 163 GLN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN A 358 ASN A 385 GLN A 449 HIS A 454 GLN A 531 ASN A 606 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 52 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.052667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.042163 restraints weight = 38068.902| |-----------------------------------------------------------------------------| r_work (start): 0.2603 rms_B_bonded: 3.40 r_work: 0.2458 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11143 Z= 0.147 Angle : 0.671 11.699 15237 Z= 0.329 Chirality : 0.044 0.255 1810 Planarity : 0.005 0.038 1831 Dihedral : 12.196 105.657 2144 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.13 % Allowed : 7.46 % Favored : 90.41 % 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: -1.01 (0.22), residues: 1303 helix: 0.50 (0.19), residues: 711 sheet: -1.10 (0.49), residues: 108 loop : -2.35 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 377 TYR 0.018 0.001 TYR C 210 PHE 0.033 0.001 PHE A 302 TRP 0.018 0.001 TRP C 227 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (11117) covalent geometry : angle 0.65084 / 0.32 (15166) SS BOND : bond 0.00456 / 0.23 ( 4) SS BOND : angle 1.19302 / 0.67 ( 8) hydrogen bonds : bond 0.04830 / 3.17 ( 573) hydrogen bonds : angle 4.54461 / 3.12 ( 1662) Misc. bond : bond 0.00145 / 0.08 ( 1) link_BETA1-3 : bond 0.00746 / 0.39 ( 1) link_BETA1-3 : angle 2.31532 / 1.77 ( 3) link_BETA1-4 : bond 0.00328 / 0.17 ( 7) link_BETA1-4 : angle 1.79805 / 1.26 ( 21) link_BETA1-6 : bond 0.01569 / 0.83 ( 1) link_BETA1-6 : angle 3.09666 / 2.57 ( 3) link_NAG-ASN : bond 0.00504 / 0.27 ( 12) link_NAG-ASN : angle 2.91000 / 2.41 ( 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 139 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.9274 (m) cc_final: 0.8722 (t) REVERT: A 83 GLN cc_start: 0.8727 (mp10) cc_final: 0.8218 (mp10) REVERT: A 95 MET cc_start: 0.8974 (ttm) cc_final: 0.8691 (ttt) REVERT: A 184 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9212 (mp0) REVERT: A 245 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8603 (mp0) REVERT: A 461 GLU cc_start: 0.9149 (mp0) cc_final: 0.8866 (mp0) REVERT: B 84 MET cc_start: 0.9277 (mtp) cc_final: 0.8892 (mtm) REVERT: B 108 ARG cc_start: 0.8601 (ttp80) cc_final: 0.8368 (ttp80) REVERT: B 110 ASP cc_start: 0.8185 (m-30) cc_final: 0.7883 (m-30) REVERT: B 128 ARG cc_start: 0.8851 (mtp180) cc_final: 0.8504 (ttp-170) REVERT: B 165 TRP cc_start: 0.8773 (t60) cc_final: 0.8565 (t60) REVERT: B 194 ASP cc_start: 0.9220 (p0) cc_final: 0.8454 (p0) REVERT: B 210 MET cc_start: 0.9397 (mmt) cc_final: 0.9083 (mmm) REVERT: B 257 ASP cc_start: 0.9341 (t70) cc_final: 0.8676 (t0) REVERT: B 403 ASP cc_start: 0.8881 (m-30) cc_final: 0.8631 (m-30) REVERT: C 28 ASP cc_start: 0.9022 (t0) cc_final: 0.8669 (t0) REVERT: C 96 LYS cc_start: 0.6188 (pttt) cc_final: 0.5822 (ptpt) REVERT: C 106 GLU cc_start: 0.9073 (tp30) cc_final: 0.8776 (tp30) REVERT: C 180 ASP cc_start: 0.9336 (t70) cc_final: 0.8781 (t0) REVERT: C 183 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8313 (tp30) REVERT: C 210 TYR cc_start: 0.9223 (m-80) cc_final: 0.9012 (m-10) REVERT: C 211 GLU cc_start: 0.9125 (pt0) cc_final: 0.8415 (pm20) REVERT: D 10 GLU cc_start: 0.8843 (mp0) cc_final: 0.8558 (mp0) REVERT: D 47 TYR cc_start: 0.8672 (p90) cc_final: 0.8207 (p90) REVERT: D 54 LYS cc_start: 0.9305 (ttpt) cc_final: 0.8944 (ttpp) outliers start: 24 outliers final: 10 residues processed: 127 average time/residue: 0.4700 time to fit residues: 65.2807 Evaluate side-chains 107 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain D residue 77 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 67 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 106 optimal weight: 0.2980 chunk 64 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS B 127 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.051367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.040756 restraints weight = 38388.479| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 3.41 r_work: 0.2410 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11143 Z= 0.185 Angle : 0.643 11.531 15237 Z= 0.314 Chirality : 0.043 0.233 1810 Planarity : 0.004 0.041 1831 Dihedral : 10.499 114.517 2144 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.51 % Allowed : 9.86 % Favored : 88.63 % 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: 0.09 (0.24), residues: 1303 helix: 1.46 (0.20), residues: 723 sheet: -0.86 (0.49), residues: 110 loop : -2.01 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 377 TYR 0.015 0.001 TYR C 210 PHE 0.031 0.002 PHE A 302 TRP 0.011 0.001 TRP D 36 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (11117) covalent geometry : angle 0.62733 / 0.31 (15166) SS BOND : bond 0.00456 / 0.23 ( 4) SS BOND : angle 1.11670 / 0.61 ( 8) hydrogen bonds : bond 0.04410 / 2.89 ( 573) hydrogen bonds : angle 4.13576 / 2.86 ( 1662) Misc. bond : bond 0.00192 / 0.10 ( 1) link_BETA1-3 : bond 0.00632 / 0.33 ( 1) link_BETA1-3 : angle 1.88511 / 1.23 ( 3) link_BETA1-4 : bond 0.00214 / 0.11 ( 7) link_BETA1-4 : angle 1.75061 / 1.25 ( 21) link_BETA1-6 : bond 0.01609 / 0.85 ( 1) link_BETA1-6 : angle 2.97467 / 2.50 ( 3) link_NAG-ASN : bond 0.00418 / 0.22 ( 12) link_NAG-ASN : angle 2.44907 / 2.11 ( 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 114 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8601 (mp0) REVERT: A 343 MET cc_start: 0.9494 (tpp) cc_final: 0.9242 (ttm) REVERT: A 461 GLU cc_start: 0.9185 (mp0) cc_final: 0.8882 (mp0) REVERT: B 84 MET cc_start: 0.9290 (mtp) cc_final: 0.8915 (mtm) REVERT: B 110 ASP cc_start: 0.8056 (m-30) cc_final: 0.7768 (m-30) REVERT: B 194 ASP cc_start: 0.9224 (p0) cc_final: 0.8470 (p0) REVERT: B 210 MET cc_start: 0.9380 (mmt) cc_final: 0.9178 (mmm) REVERT: B 257 ASP cc_start: 0.9361 (t70) cc_final: 0.8670 (t0) REVERT: B 273 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8757 (mp0) REVERT: B 403 ASP cc_start: 0.8915 (m-30) cc_final: 0.8679 (m-30) REVERT: B 454 GLN cc_start: 0.9116 (tp40) cc_final: 0.8883 (tp-100) REVERT: C 28 ASP cc_start: 0.9123 (t0) cc_final: 0.8672 (t70) REVERT: C 96 LYS cc_start: 0.6234 (pttt) cc_final: 0.6007 (ptpt) REVERT: C 99 GLU cc_start: 0.8613 (pp20) cc_final: 0.8389 (pt0) REVERT: C 106 GLU cc_start: 0.9067 (tp30) cc_final: 0.8698 (tp30) REVERT: C 180 ASP cc_start: 0.9313 (t70) cc_final: 0.8776 (t0) REVERT: C 183 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8400 (tp30) REVERT: C 211 GLU cc_start: 0.9135 (pt0) cc_final: 0.8438 (pm20) REVERT: D 47 TYR cc_start: 0.8683 (p90) cc_final: 0.7899 (p90) REVERT: D 49 GLU cc_start: 0.9364 (mm-30) cc_final: 0.8920 (mp0) REVERT: D 54 LYS cc_start: 0.9193 (ttpt) cc_final: 0.8866 (ttpp) outliers start: 17 outliers final: 8 residues processed: 109 average time/residue: 0.5911 time to fit residues: 69.7875 Evaluate side-chains 96 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 77 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 99 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.052007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.041426 restraints weight = 37989.142| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 3.37 r_work: 0.2431 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11143 Z= 0.140 Angle : 0.593 11.003 15237 Z= 0.290 Chirality : 0.042 0.230 1810 Planarity : 0.003 0.041 1831 Dihedral : 9.847 112.225 2144 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.78 % Allowed : 10.39 % Favored : 87.83 % 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: 0.62 (0.24), residues: 1303 helix: 1.91 (0.20), residues: 723 sheet: -0.67 (0.49), residues: 108 loop : -1.79 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 377 TYR 0.019 0.001 TYR C 210 PHE 0.029 0.001 PHE A 302 TRP 0.009 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (11117) covalent geometry : angle 0.57875 / 0.29 (15166) SS BOND : bond 0.00387 / 0.19 ( 4) SS BOND : angle 1.01460 / 0.55 ( 8) hydrogen bonds : bond 0.03891 / 2.55 ( 573) hydrogen bonds : angle 3.93690 / 2.74 ( 1662) Misc. bond : bond 0.00172 / 0.09 ( 1) link_BETA1-3 : bond 0.00643 / 0.34 ( 1) link_BETA1-3 : angle 2.05350 / 1.20 ( 3) link_BETA1-4 : bond 0.00260 / 0.13 ( 7) link_BETA1-4 : angle 1.59377 / 1.11 ( 21) link_BETA1-6 : bond 0.01311 / 0.69 ( 1) link_BETA1-6 : angle 3.05784 / 2.73 ( 3) link_NAG-ASN : bond 0.00362 / 0.19 ( 12) link_NAG-ASN : angle 2.23429 / 1.95 ( 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 121 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.9056 (m) cc_final: 0.8559 (t) REVERT: A 245 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8594 (mp0) REVERT: A 343 MET cc_start: 0.9487 (tpp) cc_final: 0.9161 (ttm) REVERT: A 461 GLU cc_start: 0.9178 (mp0) cc_final: 0.8883 (mp0) REVERT: B 84 MET cc_start: 0.9279 (mtp) cc_final: 0.8953 (mtt) REVERT: B 110 ASP cc_start: 0.8085 (m-30) cc_final: 0.7816 (m-30) REVERT: B 112 GLN cc_start: 0.8239 (tt0) cc_final: 0.7913 (tt0) REVERT: B 194 ASP cc_start: 0.9227 (p0) cc_final: 0.8478 (p0) REVERT: B 257 ASP cc_start: 0.9370 (t70) cc_final: 0.8672 (t0) REVERT: B 403 ASP cc_start: 0.8914 (m-30) cc_final: 0.8700 (m-30) REVERT: C 28 ASP cc_start: 0.9127 (t0) cc_final: 0.8660 (t70) REVERT: C 96 LYS cc_start: 0.6092 (pttt) cc_final: 0.5640 (ttpt) REVERT: C 106 GLU cc_start: 0.9082 (tp30) cc_final: 0.8650 (tp30) REVERT: C 180 ASP cc_start: 0.9271 (t70) cc_final: 0.8744 (t0) REVERT: C 211 GLU cc_start: 0.9121 (pt0) cc_final: 0.8455 (pm20) REVERT: D 47 TYR cc_start: 0.8632 (p90) cc_final: 0.7836 (p90) REVERT: D 49 GLU cc_start: 0.9370 (mm-30) cc_final: 0.8985 (mp0) REVERT: D 54 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8773 (ttpp) outliers start: 20 outliers final: 10 residues processed: 116 average time/residue: 0.5437 time to fit residues: 68.5232 Evaluate side-chains 103 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 77 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.052485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.041888 restraints weight = 37961.239| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 3.39 r_work: 0.2442 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11143 Z= 0.119 Angle : 0.583 10.543 15237 Z= 0.285 Chirality : 0.041 0.241 1810 Planarity : 0.003 0.041 1831 Dihedral : 9.459 106.758 2144 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.76 % Favored : 97.16 % Rotamer: Outliers : 1.15 % Allowed : 11.81 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.88 (0.24), residues: 1303 helix: 2.12 (0.20), residues: 723 sheet: -0.68 (0.49), residues: 111 loop : -1.64 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 377 TYR 0.019 0.001 TYR C 210 PHE 0.027 0.001 PHE A 302 TRP 0.008 0.001 TRP D 36 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (11117) covalent geometry : angle 0.57021 / 0.28 (15166) SS BOND : bond 0.00320 / 0.16 ( 4) SS BOND : angle 0.94867 / 0.53 ( 8) hydrogen bonds : bond 0.03614 / 2.38 ( 573) hydrogen bonds : angle 3.84783 / 2.67 ( 1662) Misc. bond : bond 0.00167 / 0.09 ( 1) link_BETA1-3 : bond 0.00677 / 0.36 ( 1) link_BETA1-3 : angle 1.97556 / 1.13 ( 3) link_BETA1-4 : bond 0.00243 / 0.13 ( 7) link_BETA1-4 : angle 1.49055 / 1.03 ( 21) link_BETA1-6 : bond 0.01472 / 0.77 ( 1) link_BETA1-6 : angle 3.19915 / 2.83 ( 3) link_NAG-ASN : bond 0.00334 / 0.18 ( 12) link_NAG-ASN : angle 2.08824 / 1.83 ( 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 109 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8591 (mp0) REVERT: A 343 MET cc_start: 0.9498 (tpp) cc_final: 0.9206 (ttm) REVERT: A 461 GLU cc_start: 0.9175 (mp0) cc_final: 0.8891 (mp0) REVERT: B 84 MET cc_start: 0.9281 (mtp) cc_final: 0.8909 (mtt) REVERT: B 108 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8202 (ttm170) REVERT: B 112 GLN cc_start: 0.8213 (tt0) cc_final: 0.7880 (tt0) REVERT: B 194 ASP cc_start: 0.9242 (p0) cc_final: 0.8476 (p0) REVERT: B 257 ASP cc_start: 0.9374 (t70) cc_final: 0.8664 (t0) REVERT: B 273 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8737 (mp0) REVERT: B 458 ASP cc_start: 0.9386 (t0) cc_final: 0.8976 (t0) REVERT: C 28 ASP cc_start: 0.9135 (t0) cc_final: 0.8653 (t70) REVERT: C 106 GLU cc_start: 0.9069 (tp30) cc_final: 0.8634 (tp30) REVERT: C 180 ASP cc_start: 0.9254 (t70) cc_final: 0.8722 (t0) REVERT: C 211 GLU cc_start: 0.9119 (pt0) cc_final: 0.8450 (pm20) REVERT: D 47 TYR cc_start: 0.8606 (p90) cc_final: 0.7771 (p90) REVERT: D 49 GLU cc_start: 0.9388 (mm-30) cc_final: 0.8997 (mp0) REVERT: D 54 LYS cc_start: 0.9093 (ttpt) cc_final: 0.8785 (ttpp) outliers start: 13 outliers final: 10 residues processed: 105 average time/residue: 0.5528 time to fit residues: 63.1678 Evaluate side-chains 99 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 77 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 25 optimal weight: 4.9990 chunk 111 optimal weight: 0.0030 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN B 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.050270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.039608 restraints weight = 38649.181| |-----------------------------------------------------------------------------| r_work (start): 0.2528 rms_B_bonded: 3.39 r_work: 0.2379 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11143 Z= 0.260 Angle : 0.666 10.345 15237 Z= 0.327 Chirality : 0.044 0.224 1810 Planarity : 0.004 0.045 1831 Dihedral : 9.486 99.805 2144 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 2.13 % Allowed : 11.55 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.02 (0.24), residues: 1303 helix: 2.26 (0.20), residues: 722 sheet: -0.65 (0.49), residues: 109 loop : -1.61 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 626 TYR 0.019 0.001 TYR C 210 PHE 0.027 0.002 PHE A 302 TRP 0.012 0.001 TRP C 209 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.26 (11117) covalent geometry : angle 0.65210 / 0.32 (15166) SS BOND : bond 0.00598 / 0.30 ( 4) SS BOND : angle 1.25763 / 0.63 ( 8) hydrogen bonds : bond 0.04066 / 2.64 ( 573) hydrogen bonds : angle 3.93809 / 2.74 ( 1662) Misc. bond : bond 0.00191 / 0.10 ( 1) link_BETA1-3 : bond 0.00342 / 0.18 ( 1) link_BETA1-3 : angle 2.27201 / 1.29 ( 3) link_BETA1-4 : bond 0.00163 / 0.08 ( 7) link_BETA1-4 : angle 1.62236 / 1.12 ( 21) link_BETA1-6 : bond 0.01465 / 0.77 ( 1) link_BETA1-6 : angle 3.47520 / 3.05 ( 3) link_NAG-ASN : bond 0.00426 / 0.23 ( 12) link_NAG-ASN : angle 2.35294 / 2.04 ( 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 116 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.8912 (m) cc_final: 0.8665 (t) REVERT: A 245 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8559 (mp0) REVERT: A 343 MET cc_start: 0.9479 (tpp) cc_final: 0.9240 (ttm) REVERT: A 461 GLU cc_start: 0.9185 (mp0) cc_final: 0.8896 (mp0) REVERT: B 84 MET cc_start: 0.9225 (mtp) cc_final: 0.8877 (mtt) REVERT: B 108 ARG cc_start: 0.8874 (ttp80) cc_final: 0.8200 (ptt-90) REVERT: B 110 ASP cc_start: 0.8039 (m-30) cc_final: 0.7747 (m-30) REVERT: B 112 GLN cc_start: 0.8125 (tt0) cc_final: 0.7839 (tt0) REVERT: B 128 ARG cc_start: 0.8952 (mtp180) cc_final: 0.8339 (ttp-170) REVERT: B 194 ASP cc_start: 0.9162 (p0) cc_final: 0.8320 (p0) REVERT: B 243 GLU cc_start: 0.8053 (pm20) cc_final: 0.7845 (pm20) REVERT: B 257 ASP cc_start: 0.9435 (t70) cc_final: 0.8742 (t0) REVERT: B 273 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8821 (mp0) REVERT: B 458 ASP cc_start: 0.9426 (t0) cc_final: 0.9202 (t0) REVERT: C 28 ASP cc_start: 0.9115 (t0) cc_final: 0.8857 (t0) REVERT: C 106 GLU cc_start: 0.9068 (tp30) cc_final: 0.8667 (tp30) REVERT: C 180 ASP cc_start: 0.9257 (t70) cc_final: 0.8740 (t0) REVERT: C 211 GLU cc_start: 0.9218 (pt0) cc_final: 0.8576 (pm20) REVERT: D 47 TYR cc_start: 0.8673 (p90) cc_final: 0.7739 (p90) REVERT: D 49 GLU cc_start: 0.9429 (mm-30) cc_final: 0.8894 (mp0) REVERT: D 54 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8747 (ttpp) outliers start: 24 outliers final: 13 residues processed: 111 average time/residue: 0.5023 time to fit residues: 60.7719 Evaluate side-chains 101 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 128 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.050709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.040094 restraints weight = 38244.146| |-----------------------------------------------------------------------------| r_work (start): 0.2536 rms_B_bonded: 3.36 r_work: 0.2389 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11143 Z= 0.178 Angle : 0.632 10.250 15237 Z= 0.309 Chirality : 0.042 0.228 1810 Planarity : 0.003 0.045 1831 Dihedral : 9.237 89.849 2144 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.07 % Favored : 96.85 % Rotamer: Outliers : 1.15 % Allowed : 13.06 % Favored : 85.79 % 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: 1.18 (0.25), residues: 1303 helix: 2.35 (0.20), residues: 722 sheet: -0.60 (0.50), residues: 109 loop : -1.47 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 626 TYR 0.018 0.001 TYR C 156 PHE 0.027 0.001 PHE A 302 TRP 0.009 0.001 TRP C 209 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (11117) covalent geometry : angle 0.61901 / 0.31 (15166) SS BOND : bond 0.00572 / 0.29 ( 4) SS BOND : angle 1.14599 / 0.59 ( 8) hydrogen bonds : bond 0.03885 / 2.53 ( 573) hydrogen bonds : angle 3.87252 / 2.69 ( 1662) Misc. bond : bond 0.00189 / 0.10 ( 1) link_BETA1-3 : bond 0.00454 / 0.24 ( 1) link_BETA1-3 : angle 2.18892 / 1.25 ( 3) link_BETA1-4 : bond 0.00144 / 0.07 ( 7) link_BETA1-4 : angle 1.46945 / 1.01 ( 21) link_BETA1-6 : bond 0.01416 / 0.75 ( 1) link_BETA1-6 : angle 3.52829 / 3.01 ( 3) link_NAG-ASN : bond 0.00326 / 0.17 ( 12) link_NAG-ASN : angle 2.19183 / 1.91 ( 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 107 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8556 (mp0) REVERT: A 343 MET cc_start: 0.9474 (tpp) cc_final: 0.9235 (ttm) REVERT: A 461 GLU cc_start: 0.9195 (mp0) cc_final: 0.8902 (mp0) REVERT: B 84 MET cc_start: 0.9214 (mtp) cc_final: 0.8845 (mtt) REVERT: B 108 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8072 (ptt-90) REVERT: B 110 ASP cc_start: 0.8220 (m-30) cc_final: 0.7864 (m-30) REVERT: B 112 GLN cc_start: 0.8031 (tt0) cc_final: 0.7739 (tt0) REVERT: B 128 ARG cc_start: 0.8978 (mtp180) cc_final: 0.8356 (ttp-170) REVERT: B 194 ASP cc_start: 0.9174 (p0) cc_final: 0.8347 (p0) REVERT: B 243 GLU cc_start: 0.8194 (pm20) cc_final: 0.7981 (pm20) REVERT: B 257 ASP cc_start: 0.9440 (t70) cc_final: 0.8740 (t0) REVERT: B 273 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8763 (mp0) REVERT: B 458 ASP cc_start: 0.9412 (t0) cc_final: 0.9036 (t0) REVERT: C 28 ASP cc_start: 0.9115 (t0) cc_final: 0.8841 (t0) REVERT: C 106 GLU cc_start: 0.9058 (tp30) cc_final: 0.8649 (tp30) REVERT: C 180 ASP cc_start: 0.9237 (t70) cc_final: 0.8729 (t0) REVERT: C 211 GLU cc_start: 0.9236 (pt0) cc_final: 0.8603 (pm20) REVERT: D 47 TYR cc_start: 0.8581 (p90) cc_final: 0.7677 (p90) REVERT: D 49 GLU cc_start: 0.9404 (mm-30) cc_final: 0.8926 (mp0) REVERT: D 54 LYS cc_start: 0.9077 (ttpt) cc_final: 0.8746 (ttpp) outliers start: 13 outliers final: 12 residues processed: 103 average time/residue: 0.5262 time to fit residues: 58.8495 Evaluate side-chains 99 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS B 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.050956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.040277 restraints weight = 38583.110| |-----------------------------------------------------------------------------| r_work (start): 0.2529 rms_B_bonded: 3.41 r_work: 0.2380 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11143 Z= 0.197 Angle : 0.651 10.001 15237 Z= 0.316 Chirality : 0.043 0.225 1810 Planarity : 0.003 0.045 1831 Dihedral : 8.915 77.439 2144 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 1.33 % Allowed : 13.23 % Favored : 85.44 % 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: 1.23 (0.25), residues: 1303 helix: 2.37 (0.20), residues: 724 sheet: -0.56 (0.50), residues: 109 loop : -1.41 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 626 TYR 0.020 0.001 TYR C 210 PHE 0.026 0.001 PHE A 302 TRP 0.010 0.001 TRP C 209 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (11117) covalent geometry : angle 0.63758 / 0.31 (15166) SS BOND : bond 0.00567 / 0.28 ( 4) SS BOND : angle 1.20077 / 0.61 ( 8) hydrogen bonds : bond 0.03922 / 2.56 ( 573) hydrogen bonds : angle 3.86836 / 2.69 ( 1662) Misc. bond : bond 0.00199 / 0.10 ( 1) link_BETA1-3 : bond 0.00390 / 0.21 ( 1) link_BETA1-3 : angle 2.12752 / 1.22 ( 3) link_BETA1-4 : bond 0.00170 / 0.08 ( 7) link_BETA1-4 : angle 1.45698 / 1.00 ( 21) link_BETA1-6 : bond 0.01165 / 0.61 ( 1) link_BETA1-6 : angle 3.47784 / 2.65 ( 3) link_NAG-ASN : bond 0.00336 / 0.18 ( 12) link_NAG-ASN : angle 2.22029 / 1.93 ( 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 107 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8542 (mp0) REVERT: A 343 MET cc_start: 0.9470 (tpp) cc_final: 0.9226 (ttm) REVERT: A 461 GLU cc_start: 0.9212 (mp0) cc_final: 0.8921 (mp0) REVERT: B 84 MET cc_start: 0.9214 (mtp) cc_final: 0.8845 (mtt) REVERT: B 108 ARG cc_start: 0.8750 (ttp80) cc_final: 0.7971 (ptt-90) REVERT: B 110 ASP cc_start: 0.8289 (m-30) cc_final: 0.7980 (m-30) REVERT: B 112 GLN cc_start: 0.8127 (tt0) cc_final: 0.7803 (tt0) REVERT: B 128 ARG cc_start: 0.8956 (mtp180) cc_final: 0.8245 (ttp-170) REVERT: B 194 ASP cc_start: 0.9178 (p0) cc_final: 0.8321 (p0) REVERT: B 243 GLU cc_start: 0.8242 (pm20) cc_final: 0.7985 (pm20) REVERT: B 257 ASP cc_start: 0.9454 (t70) cc_final: 0.8737 (t0) REVERT: B 458 ASP cc_start: 0.9414 (t0) cc_final: 0.9054 (t0) REVERT: C 28 ASP cc_start: 0.9114 (t0) cc_final: 0.8802 (t0) REVERT: C 106 GLU cc_start: 0.9038 (tp30) cc_final: 0.8631 (tp30) REVERT: C 180 ASP cc_start: 0.9241 (t70) cc_final: 0.8743 (t0) REVERT: C 211 GLU cc_start: 0.9241 (pt0) cc_final: 0.8625 (pm20) REVERT: D 47 TYR cc_start: 0.8599 (p90) cc_final: 0.7647 (p90) REVERT: D 49 GLU cc_start: 0.9428 (mm-30) cc_final: 0.8924 (mp0) REVERT: D 54 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8709 (ttpp) outliers start: 15 outliers final: 13 residues processed: 104 average time/residue: 0.5505 time to fit residues: 62.5066 Evaluate side-chains 99 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 123 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.051157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.040525 restraints weight = 38070.544| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 3.39 r_work: 0.2400 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11143 Z= 0.147 Angle : 0.617 9.941 15237 Z= 0.302 Chirality : 0.042 0.234 1810 Planarity : 0.003 0.044 1831 Dihedral : 8.530 77.600 2144 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.07 % Favored : 96.85 % Rotamer: Outliers : 1.15 % Allowed : 13.68 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.25), residues: 1303 helix: 2.45 (0.20), residues: 724 sheet: -0.61 (0.50), residues: 111 loop : -1.34 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 626 TYR 0.018 0.001 TYR C 156 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 0.00337 / 0.15 (11117) covalent geometry : angle 0.60538 / 0.30 (15166) SS BOND : bond 0.00454 / 0.23 ( 4) SS BOND : angle 1.05921 / 0.53 ( 8) hydrogen bonds : bond 0.03682 / 2.41 ( 573) hydrogen bonds : angle 3.79827 / 2.65 ( 1662) Misc. bond : bond 0.00186 / 0.10 ( 1) link_BETA1-3 : bond 0.00543 / 0.29 ( 1) link_BETA1-3 : angle 1.76297 / 1.07 ( 3) link_BETA1-4 : bond 0.00178 / 0.09 ( 7) link_BETA1-4 : angle 1.35200 / 0.92 ( 21) link_BETA1-6 : bond 0.00973 / 0.51 ( 1) link_BETA1-6 : angle 3.42494 / 2.56 ( 3) link_NAG-ASN : bond 0.00292 / 0.15 ( 12) link_NAG-ASN : angle 2.06911 / 1.82 ( 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 104 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8551 (mp0) REVERT: A 248 CYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8716 (m) REVERT: A 343 MET cc_start: 0.9475 (tpp) cc_final: 0.9251 (ttm) REVERT: A 461 GLU cc_start: 0.9193 (mp0) cc_final: 0.8903 (mp0) REVERT: B 84 MET cc_start: 0.9194 (mtp) cc_final: 0.8835 (mtt) REVERT: B 108 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8456 (ttm170) REVERT: B 110 ASP cc_start: 0.8267 (m-30) cc_final: 0.8046 (m-30) REVERT: B 112 GLN cc_start: 0.8244 (tt0) cc_final: 0.7955 (tt0) REVERT: B 128 ARG cc_start: 0.8953 (mtp180) cc_final: 0.8260 (ttp-170) REVERT: B 194 ASP cc_start: 0.9180 (p0) cc_final: 0.8321 (p0) REVERT: B 243 GLU cc_start: 0.8228 (pm20) cc_final: 0.8018 (pm20) REVERT: B 257 ASP cc_start: 0.9442 (t70) cc_final: 0.8771 (t0) REVERT: B 458 ASP cc_start: 0.9403 (t0) cc_final: 0.9045 (t0) REVERT: C 28 ASP cc_start: 0.9105 (t0) cc_final: 0.8798 (t0) REVERT: C 106 GLU cc_start: 0.9034 (tp30) cc_final: 0.8597 (tp30) REVERT: C 180 ASP cc_start: 0.9227 (t70) cc_final: 0.8721 (t0) REVERT: C 211 GLU cc_start: 0.9249 (pt0) cc_final: 0.8616 (pm20) REVERT: D 47 TYR cc_start: 0.8537 (p90) cc_final: 0.7593 (p90) REVERT: D 49 GLU cc_start: 0.9417 (mm-30) cc_final: 0.8928 (mp0) REVERT: D 54 LYS cc_start: 0.9015 (ttpt) cc_final: 0.8674 (ttpp) outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 0.5591 time to fit residues: 60.8398 Evaluate side-chains 100 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 92 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 109 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN B 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.051466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.040818 restraints weight = 37827.657| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 3.37 r_work: 0.2416 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11143 Z= 0.137 Angle : 0.625 9.839 15237 Z= 0.305 Chirality : 0.042 0.233 1810 Planarity : 0.003 0.044 1831 Dihedral : 8.348 77.459 2144 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.99 % Favored : 96.93 % Rotamer: Outliers : 1.33 % Allowed : 13.68 % 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: 1.38 (0.25), residues: 1303 helix: 2.49 (0.20), residues: 721 sheet: -0.67 (0.50), residues: 109 loop : -1.28 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 278 TYR 0.017 0.001 TYR C 156 PHE 0.027 0.001 PHE A 302 TRP 0.011 0.001 TRP C 209 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (11117) covalent geometry : angle 0.61390 / 0.30 (15166) SS BOND : bond 0.00429 / 0.21 ( 4) SS BOND : angle 1.01337 / 0.51 ( 8) hydrogen bonds : bond 0.03614 / 2.37 ( 573) hydrogen bonds : angle 3.78107 / 2.63 ( 1662) Misc. bond : bond 0.00186 / 0.10 ( 1) link_BETA1-3 : bond 0.00515 / 0.27 ( 1) link_BETA1-3 : angle 1.68597 / 1.03 ( 3) link_BETA1-4 : bond 0.00182 / 0.09 ( 7) link_BETA1-4 : angle 1.35033 / 0.92 ( 21) link_BETA1-6 : bond 0.00918 / 0.48 ( 1) link_BETA1-6 : angle 3.27295 / 2.45 ( 3) link_NAG-ASN : bond 0.00289 / 0.15 ( 12) link_NAG-ASN : angle 2.03736 / 1.79 ( 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 106 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8547 (mp0) REVERT: A 248 CYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8705 (m) REVERT: A 343 MET cc_start: 0.9481 (tpp) cc_final: 0.9269 (ttm) REVERT: A 461 GLU cc_start: 0.9194 (mp0) cc_final: 0.8897 (mp0) REVERT: B 84 MET cc_start: 0.9188 (mtp) cc_final: 0.8829 (mtt) REVERT: B 108 ARG cc_start: 0.8686 (ttp80) cc_final: 0.8411 (ttm170) REVERT: B 110 ASP cc_start: 0.8255 (m-30) cc_final: 0.8009 (m-30) REVERT: B 112 GLN cc_start: 0.8273 (tt0) cc_final: 0.7955 (tt0) REVERT: B 128 ARG cc_start: 0.8944 (mtp180) cc_final: 0.8259 (ttp-170) REVERT: B 194 ASP cc_start: 0.9176 (p0) cc_final: 0.8327 (p0) REVERT: B 243 GLU cc_start: 0.8215 (pm20) cc_final: 0.7998 (pm20) REVERT: B 257 ASP cc_start: 0.9433 (t70) cc_final: 0.8743 (t0) REVERT: B 454 GLN cc_start: 0.9076 (tp40) cc_final: 0.8759 (tp40) REVERT: B 458 ASP cc_start: 0.9401 (t0) cc_final: 0.9044 (t0) REVERT: C 28 ASP cc_start: 0.9103 (t0) cc_final: 0.8793 (t0) REVERT: C 106 GLU cc_start: 0.9032 (tp30) cc_final: 0.8595 (tp30) REVERT: C 180 ASP cc_start: 0.9202 (t70) cc_final: 0.8695 (t0) REVERT: C 211 GLU cc_start: 0.9227 (pt0) cc_final: 0.8590 (pm20) REVERT: D 47 TYR cc_start: 0.8551 (p90) cc_final: 0.7587 (p90) REVERT: D 49 GLU cc_start: 0.9405 (mm-30) cc_final: 0.8951 (mp0) REVERT: D 54 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8641 (ttpp) outliers start: 15 outliers final: 14 residues processed: 103 average time/residue: 0.5461 time to fit residues: 61.2623 Evaluate side-chains 104 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 0.0170 chunk 91 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN C 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.051973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.041330 restraints weight = 38149.407| |-----------------------------------------------------------------------------| r_work (start): 0.2571 rms_B_bonded: 3.39 r_work: 0.2424 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11143 Z= 0.121 Angle : 0.605 9.821 15237 Z= 0.296 Chirality : 0.042 0.234 1810 Planarity : 0.003 0.043 1831 Dihedral : 8.189 77.351 2144 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.01 % Rotamer: Outliers : 1.07 % Allowed : 13.85 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1303 helix: 2.53 (0.20), residues: 721 sheet: -0.62 (0.51), residues: 109 loop : -1.25 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 278 TYR 0.016 0.001 TYR C 156 PHE 0.027 0.001 PHE A 302 TRP 0.010 0.001 TRP C 209 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11117) covalent geometry : angle 0.59442 / 0.29 (15166) SS BOND : bond 0.00387 / 0.19 ( 4) SS BOND : angle 0.96556 / 0.48 ( 8) hydrogen bonds : bond 0.03494 / 2.29 ( 573) hydrogen bonds : angle 3.74344 / 2.61 ( 1662) Misc. bond : bond 0.00180 / 0.09 ( 1) link_BETA1-3 : bond 0.00657 / 0.35 ( 1) link_BETA1-3 : angle 1.68198 / 1.04 ( 3) link_BETA1-4 : bond 0.00237 / 0.12 ( 7) link_BETA1-4 : angle 1.33935 / 0.92 ( 21) link_BETA1-6 : bond 0.00966 / 0.51 ( 1) link_BETA1-6 : angle 3.09069 / 2.30 ( 3) link_NAG-ASN : bond 0.00286 / 0.15 ( 12) link_NAG-ASN : angle 1.96957 / 1.72 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2600.23 seconds wall clock time: 45 minutes 24.27 seconds (2724.27 seconds total)