Starting phenix.real_space_refine on Wed Mar 4 06:36:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c9i_30312/03_2026/7c9i_30312.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c9i_30312/03_2026/7c9i_30312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c9i_30312/03_2026/7c9i_30312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c9i_30312/03_2026/7c9i_30312.map" model { file = "/net/cci-nas-00/data/ceres_data/7c9i_30312/03_2026/7c9i_30312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c9i_30312/03_2026/7c9i_30312.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 40 5.16 5 C 7123 2.51 5 N 1709 2.21 5 O 1979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10853 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: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'FTO': 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: 2.51, per 1000 atoms: 0.23 Number of scatterers: 10853 At special positions: 0 Unit cell: (110.191, 93.826, 133.102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 2 15.00 O 1979 8.00 N 1709 7.00 C 7123 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=2.04 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=0, 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 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 503.8 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: 49 helices and 6 sheets defined 57.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.578A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 87 removed outlier: 4.064A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.732A pdb=" N MET A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.904A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.715A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.120A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.511A pdb=" N SER A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 313 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 407 removed outlier: 4.096A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 481 through 503 removed outlier: 3.797A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.780A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.701A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.530A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.671A pdb=" N ASP A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.731A pdb=" N GLU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.554A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.505A pdb=" N PHE A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 103 removed outlier: 3.581A pdb=" N VAL B 87 " --> pdb=" O ILE B 83 " (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 159 through 176 removed outlier: 3.924A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 removed outlier: 3.500A pdb=" N GLN B 222 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.770A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.965A pdb=" N MET B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.640A pdb=" N THR B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 429 removed outlier: 3.746A pdb=" N THR B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 408 " --> pdb=" O TRP B 404 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 4.424A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 4.229A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.612A pdb=" N PHE C 11 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 Processing helix chain 'C' and resid 30 through 61 removed outlier: 3.511A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 103 removed outlier: 3.597A pdb=" N TYR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 139 removed outlier: 3.704A pdb=" N MET C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.767A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 203 removed outlier: 4.111A 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 214 through 232 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 21 removed outlier: 3.550A pdb=" N GLY D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.820A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 82 removed outlier: 4.029A pdb=" N GLY D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU D 71 " --> pdb=" O TRP D 67 " (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: 4.596A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.685A 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: 3.636A pdb=" N MET A 378 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.745A 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: 4.262A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 603 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.603A 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 289 545 hydrogen bonds defined for protein. 1587 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: 1.66 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1639 1.31 - 1.44: 3156 1.44 - 1.56: 6269 1.56 - 1.69: 8 1.69 - 1.81: 61 Bond restraints: 11133 Sorted by residual: bond pdb=" C16 FTO B 502 " pdb=" N17 FTO B 502 " ideal model delta sigma weight residual 1.337 1.451 -0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C13 FTO B 502 " pdb=" N14 FTO B 502 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C10 FTO B 502 " pdb=" N11 FTO B 502 " ideal model delta sigma weight residual 1.347 1.452 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C04 FTO B 502 " pdb=" N05 FTO B 502 " ideal model delta sigma weight residual 1.350 1.452 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C04 FTO B 502 " pdb=" O03 FTO B 502 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 11128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 14863 3.10 - 6.19: 279 6.19 - 9.29: 33 9.29 - 12.38: 9 12.38 - 15.48: 1 Bond angle restraints: 15185 Sorted by residual: angle pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta sigma weight residual 121.97 131.19 -9.22 1.80e+00 3.09e-01 2.62e+01 angle pdb=" C PHE B 86 " pdb=" N VAL B 87 " pdb=" CA VAL B 87 " ideal model delta sigma weight residual 120.33 124.40 -4.07 8.00e-01 1.56e+00 2.59e+01 angle pdb=" CA LEU B 286 " pdb=" CB LEU B 286 " pdb=" CG LEU B 286 " ideal model delta sigma weight residual 116.30 131.78 -15.48 3.50e+00 8.16e-02 1.96e+01 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 115.79 -5.09 1.22e+00 6.72e-01 1.74e+01 angle pdb=" N ALA A 157 " pdb=" CA ALA A 157 " pdb=" C ALA A 157 " ideal model delta sigma weight residual 110.97 115.28 -4.31 1.09e+00 8.42e-01 1.56e+01 ... (remaining 15180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.70: 6625 22.70 - 45.40: 197 45.40 - 68.10: 49 68.10 - 90.80: 24 90.80 - 113.51: 18 Dihedral angle restraints: 6913 sinusoidal: 3080 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 -167.45 81.45 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta harmonic sigma weight residual -180.00 -142.30 -37.70 0 5.00e+00 4.00e-02 5.68e+01 dihedral pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 145.95 -52.95 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 6910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1628 0.096 - 0.191: 168 0.191 - 0.287: 12 0.287 - 0.383: 4 0.383 - 0.478: 1 Chirality restraints: 1813 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 -1.92 -0.48 2.00e-01 2.50e+01 5.72e+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 -2.12 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C3 NAG A 804 " pdb=" N2 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 1810 not shown) Planarity restraints: 1845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.027 2.00e-02 2.50e+03 2.11e-02 1.12e+01 pdb=" CG TRP C 227 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 36 " -0.024 2.00e-02 2.50e+03 1.83e-02 8.37e+00 pdb=" CG TRP D 36 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 36 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 36 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 36 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 36 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 36 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+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 " -0.041 5.00e-02 4.00e+02 ... (remaining 1842 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1900 2.77 - 3.30: 9669 3.30 - 3.83: 17429 3.83 - 4.37: 20748 4.37 - 4.90: 36534 Nonbonded interactions: 86280 Sorted by model distance: nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.232 3.040 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.240 3.040 nonbonded pdb=" O PHE B 445 " pdb=" OG1 THR B 449 " model vdw 2.282 3.040 nonbonded pdb=" OG SER D 7 " pdb=" OE1 GLU D 9 " model vdw 2.293 3.040 nonbonded pdb=" O GLU D 40 " pdb=" OH TYR D 47 " model vdw 2.303 3.040 ... (remaining 86275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.020 Process input model: 10.840 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 0.114 11158 Z= 0.353 Angle : 1.096 15.481 15256 Z= 0.551 Chirality : 0.062 0.478 1813 Planarity : 0.008 0.071 1833 Dihedral : 14.169 113.506 4431 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.18 % Allowed : 2.04 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.93 (0.18), residues: 1303 helix: -2.14 (0.15), residues: 702 sheet: -1.99 (0.40), residues: 125 loop : -3.33 (0.22), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 429 TYR 0.038 0.003 TYR A 565 PHE 0.038 0.004 PHE C 132 TRP 0.055 0.004 TRP C 227 HIS 0.026 0.003 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00788 (11133) covalent geometry : angle 1.06473 (15185) SS BOND : bond 0.00526 ( 4) SS BOND : angle 2.15415 ( 8) hydrogen bonds : bond 0.18515 ( 545) hydrogen bonds : angle 6.91153 ( 1587) link_BETA1-3 : bond 0.00062 ( 1) link_BETA1-3 : angle 1.42955 ( 3) link_BETA1-4 : bond 0.00603 ( 7) link_BETA1-4 : angle 2.60600 ( 21) link_BETA1-6 : bond 0.00405 ( 1) link_BETA1-6 : angle 1.49457 ( 3) link_NAG-ASN : bond 0.01070 ( 12) link_NAG-ASN : angle 5.05670 ( 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 199 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 0.386 Fit side-chains REVERT: A 246 ILE cc_start: 0.8339 (mm) cc_final: 0.8096 (mt) REVERT: A 693 LYS cc_start: 0.8779 (mmtp) cc_final: 0.8549 (mmtp) REVERT: B 165 TRP cc_start: 0.7283 (t60) cc_final: 0.6738 (t60) REVERT: B 169 SER cc_start: 0.9116 (t) cc_final: 0.8475 (p) REVERT: C 237 ARG cc_start: 0.7047 (mtt180) cc_final: 0.6781 (mtt-85) REVERT: D 54 LYS cc_start: 0.7488 (ttpt) cc_final: 0.6874 (ttpp) REVERT: D 91 TYR cc_start: 0.7591 (m-80) cc_final: 0.6970 (m-80) outliers start: 2 outliers final: 2 residues processed: 198 average time/residue: 0.1181 time to fit residues: 31.7712 Evaluate side-chains 132 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 380 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 222 HIS A 355 GLN A 385 GLN A 454 GLN A 531 ASN A 606 GLN B 454 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.139015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114213 restraints weight = 13623.979| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.83 r_work: 0.2981 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11158 Z= 0.156 Angle : 0.700 11.982 15256 Z= 0.337 Chirality : 0.045 0.260 1813 Planarity : 0.005 0.048 1833 Dihedral : 12.957 115.493 2127 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.60 % Allowed : 6.13 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.89 (0.21), residues: 1303 helix: -0.18 (0.19), residues: 713 sheet: -1.77 (0.40), residues: 122 loop : -2.77 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 391 TYR 0.014 0.002 TYR A 337 PHE 0.034 0.002 PHE A 302 TRP 0.021 0.002 TRP C 209 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00361 (11133) covalent geometry : angle 0.67710 (15185) SS BOND : bond 0.00603 ( 4) SS BOND : angle 1.09820 ( 8) hydrogen bonds : bond 0.05461 ( 545) hydrogen bonds : angle 4.48501 ( 1587) link_BETA1-3 : bond 0.00956 ( 1) link_BETA1-3 : angle 1.98206 ( 3) link_BETA1-4 : bond 0.00464 ( 7) link_BETA1-4 : angle 1.74665 ( 21) link_BETA1-6 : bond 0.01197 ( 1) link_BETA1-6 : angle 2.23589 ( 3) link_NAG-ASN : bond 0.00550 ( 12) link_NAG-ASN : angle 3.36351 ( 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 156 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.246 Fit side-chains REVERT: A 99 GLU cc_start: 0.8310 (tp30) cc_final: 0.8095 (tt0) REVERT: A 237 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7524 (mm-40) REVERT: A 246 ILE cc_start: 0.8526 (mm) cc_final: 0.8283 (mt) REVERT: A 343 MET cc_start: 0.9072 (tpp) cc_final: 0.8678 (tpp) REVERT: A 474 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7689 (tm-30) REVERT: A 636 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7679 (mm-30) REVERT: A 693 LYS cc_start: 0.8827 (mmtp) cc_final: 0.8587 (mmtp) REVERT: B 80 LYS cc_start: 0.8580 (tttt) cc_final: 0.8064 (tppt) REVERT: B 165 TRP cc_start: 0.7657 (t60) cc_final: 0.7073 (t60) REVERT: B 169 SER cc_start: 0.9183 (t) cc_final: 0.8671 (p) REVERT: B 210 MET cc_start: 0.9052 (mmt) cc_final: 0.8383 (mmt) REVERT: C 140 ASP cc_start: 0.8579 (m-30) cc_final: 0.8359 (m-30) REVERT: C 237 ARG cc_start: 0.7042 (mtt180) cc_final: 0.6748 (mtt-85) REVERT: D 8 ASN cc_start: 0.7569 (m110) cc_final: 0.7351 (m-40) REVERT: D 34 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8193 (mp) REVERT: D 54 LYS cc_start: 0.7358 (ttpt) cc_final: 0.6997 (ttpp) REVERT: D 91 TYR cc_start: 0.7967 (m-80) cc_final: 0.7535 (m-80) outliers start: 18 outliers final: 11 residues processed: 150 average time/residue: 0.1059 time to fit residues: 22.2067 Evaluate side-chains 132 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 220 HIS A 610 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.133604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108646 restraints weight = 13732.146| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.84 r_work: 0.2920 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11158 Z= 0.212 Angle : 0.725 14.242 15256 Z= 0.347 Chirality : 0.047 0.245 1813 Planarity : 0.005 0.055 1833 Dihedral : 11.121 114.982 2123 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.58 % Allowed : 8.61 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.05 (0.22), residues: 1303 helix: 0.64 (0.20), residues: 707 sheet: -1.59 (0.40), residues: 127 loop : -2.54 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 233 TYR 0.017 0.002 TYR A 645 PHE 0.036 0.002 PHE A 302 TRP 0.020 0.002 TRP C 209 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00520 (11133) covalent geometry : angle 0.70524 (15185) SS BOND : bond 0.00807 ( 4) SS BOND : angle 0.93305 ( 8) hydrogen bonds : bond 0.05385 ( 545) hydrogen bonds : angle 4.22546 ( 1587) link_BETA1-3 : bond 0.00903 ( 1) link_BETA1-3 : angle 1.54935 ( 3) link_BETA1-4 : bond 0.00299 ( 7) link_BETA1-4 : angle 1.88496 ( 21) link_BETA1-6 : bond 0.01430 ( 1) link_BETA1-6 : angle 2.31167 ( 3) link_NAG-ASN : bond 0.00486 ( 12) link_NAG-ASN : angle 3.16714 ( 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 145 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.437 Fit side-chains REVERT: A 99 GLU cc_start: 0.8350 (tp30) cc_final: 0.8087 (tt0) REVERT: A 160 ARG cc_start: 0.8771 (ptp-170) cc_final: 0.8519 (ptp-170) REVERT: A 215 MET cc_start: 0.9212 (ttm) cc_final: 0.8974 (ttp) REVERT: A 343 MET cc_start: 0.9079 (tpp) cc_final: 0.8816 (tpp) REVERT: A 474 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7836 (tm-30) REVERT: A 693 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8639 (mmtp) REVERT: A 699 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7398 (pp) REVERT: B 80 LYS cc_start: 0.8605 (tttt) cc_final: 0.8101 (tppt) REVERT: B 159 TYR cc_start: 0.6347 (m-80) cc_final: 0.6001 (m-80) REVERT: B 165 TRP cc_start: 0.7724 (t60) cc_final: 0.7516 (t60) REVERT: B 169 SER cc_start: 0.9165 (t) cc_final: 0.8606 (p) REVERT: B 210 MET cc_start: 0.8927 (mmt) cc_final: 0.8401 (mmt) REVERT: C 140 ASP cc_start: 0.8634 (m-30) cc_final: 0.8417 (m-30) REVERT: C 237 ARG cc_start: 0.7065 (mtt180) cc_final: 0.6715 (mtt-85) REVERT: D 34 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8233 (mp) REVERT: D 91 TYR cc_start: 0.8080 (m-80) cc_final: 0.7632 (m-80) outliers start: 29 outliers final: 18 residues processed: 137 average time/residue: 0.1147 time to fit residues: 21.9089 Evaluate side-chains 128 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG 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 119 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN B 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.101051 restraints weight = 14123.229| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.94 r_work: 0.2927 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 11158 Z= 0.142 Angle : 0.635 13.077 15256 Z= 0.305 Chirality : 0.044 0.248 1813 Planarity : 0.004 0.043 1833 Dihedral : 10.172 112.448 2123 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.31 % Allowed : 10.21 % Favored : 87.48 % 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: -0.51 (0.23), residues: 1303 helix: 1.11 (0.20), residues: 711 sheet: -1.52 (0.42), residues: 119 loop : -2.32 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.014 0.001 TYR A 569 PHE 0.031 0.001 PHE A 302 TRP 0.010 0.001 TRP C 209 HIS 0.004 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00343 (11133) covalent geometry : angle 0.61836 (15185) SS BOND : bond 0.00306 ( 4) SS BOND : angle 0.94849 ( 8) hydrogen bonds : bond 0.04393 ( 545) hydrogen bonds : angle 4.01547 ( 1587) link_BETA1-3 : bond 0.00815 ( 1) link_BETA1-3 : angle 1.21783 ( 3) link_BETA1-4 : bond 0.00366 ( 7) link_BETA1-4 : angle 1.72579 ( 21) link_BETA1-6 : bond 0.01123 ( 1) link_BETA1-6 : angle 2.08352 ( 3) link_NAG-ASN : bond 0.00429 ( 12) link_NAG-ASN : angle 2.71796 ( 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 137 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.474 Fit side-chains REVERT: A 99 GLU cc_start: 0.8306 (tp30) cc_final: 0.8052 (tt0) REVERT: A 253 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8356 (t70) REVERT: A 343 MET cc_start: 0.9063 (tpp) cc_final: 0.8666 (tpp) REVERT: A 693 LYS cc_start: 0.8990 (mmtp) cc_final: 0.8742 (mmtp) REVERT: A 699 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7440 (pp) REVERT: B 80 LYS cc_start: 0.8539 (tttt) cc_final: 0.8066 (tppt) REVERT: B 159 TYR cc_start: 0.6350 (m-80) cc_final: 0.6069 (m-80) REVERT: B 169 SER cc_start: 0.9172 (t) cc_final: 0.8672 (p) REVERT: B 241 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7239 (mp) REVERT: B 280 GLU cc_start: 0.6293 (pt0) cc_final: 0.6058 (pt0) REVERT: C 138 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8304 (mp) REVERT: C 140 ASP cc_start: 0.8682 (m-30) cc_final: 0.8475 (m-30) REVERT: C 214 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7992 (mp) REVERT: C 230 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8349 (mm) REVERT: C 237 ARG cc_start: 0.7052 (mtt180) cc_final: 0.6761 (mtt-85) REVERT: D 80 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8123 (mp) REVERT: D 91 TYR cc_start: 0.8024 (m-80) cc_final: 0.7578 (m-80) outliers start: 26 outliers final: 15 residues processed: 131 average time/residue: 0.1150 time to fit residues: 20.9592 Evaluate side-chains 132 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 28 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN B 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.101680 restraints weight = 14142.282| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.94 r_work: 0.2932 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11158 Z= 0.128 Angle : 0.605 12.730 15256 Z= 0.290 Chirality : 0.043 0.248 1813 Planarity : 0.004 0.041 1833 Dihedral : 9.514 109.154 2123 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.93 % Allowed : 10.48 % Favored : 86.59 % 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: -0.14 (0.24), residues: 1303 helix: 1.41 (0.20), residues: 713 sheet: -1.24 (0.41), residues: 130 loop : -2.22 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.014 0.001 TYR A 569 PHE 0.030 0.001 PHE A 302 TRP 0.010 0.001 TRP D 58 HIS 0.004 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00302 (11133) covalent geometry : angle 0.58807 (15185) SS BOND : bond 0.00265 ( 4) SS BOND : angle 0.74907 ( 8) hydrogen bonds : bond 0.04076 ( 545) hydrogen bonds : angle 3.87705 ( 1587) link_BETA1-3 : bond 0.00762 ( 1) link_BETA1-3 : angle 1.82264 ( 3) link_BETA1-4 : bond 0.00271 ( 7) link_BETA1-4 : angle 1.71707 ( 21) link_BETA1-6 : bond 0.01140 ( 1) link_BETA1-6 : angle 3.20176 ( 3) link_NAG-ASN : bond 0.00399 ( 12) link_NAG-ASN : angle 2.45386 ( 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 154 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.367 Fit side-chains REVERT: A 99 GLU cc_start: 0.8281 (tp30) cc_final: 0.8031 (tt0) REVERT: A 215 MET cc_start: 0.9276 (ttm) cc_final: 0.9051 (ttp) REVERT: A 253 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8319 (t70) REVERT: A 343 MET cc_start: 0.9053 (tpp) cc_final: 0.8677 (tpp) REVERT: A 693 LYS cc_start: 0.8994 (mmtp) cc_final: 0.8747 (mmtp) REVERT: A 699 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7503 (pp) REVERT: B 80 LYS cc_start: 0.8557 (tttt) cc_final: 0.8077 (tppt) REVERT: B 169 SER cc_start: 0.9130 (t) cc_final: 0.8629 (p) REVERT: B 241 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7078 (mp) REVERT: B 280 GLU cc_start: 0.6237 (pt0) cc_final: 0.6013 (pt0) REVERT: C 140 ASP cc_start: 0.8674 (m-30) cc_final: 0.8463 (m-30) REVERT: C 230 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8349 (mm) REVERT: C 237 ARG cc_start: 0.6989 (mtt180) cc_final: 0.6720 (mtt-85) REVERT: D 80 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8197 (mp) REVERT: D 91 TYR cc_start: 0.7943 (m-80) cc_final: 0.7607 (m-80) outliers start: 33 outliers final: 21 residues processed: 146 average time/residue: 0.1006 time to fit residues: 20.9186 Evaluate side-chains 139 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 63 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 66 optimal weight: 0.0000 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113361 restraints weight = 13611.925| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.79 r_work: 0.2990 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11158 Z= 0.129 Angle : 0.604 12.702 15256 Z= 0.288 Chirality : 0.043 0.245 1813 Planarity : 0.004 0.039 1833 Dihedral : 9.119 96.522 2123 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.11 % Allowed : 11.19 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.24), residues: 1303 helix: 1.58 (0.20), residues: 713 sheet: -1.11 (0.42), residues: 130 loop : -2.12 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.014 0.001 TYR A 569 PHE 0.030 0.001 PHE A 302 TRP 0.008 0.001 TRP C 209 HIS 0.003 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00305 (11133) covalent geometry : angle 0.58836 (15185) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.66324 ( 8) hydrogen bonds : bond 0.04014 ( 545) hydrogen bonds : angle 3.80263 ( 1587) link_BETA1-3 : bond 0.00752 ( 1) link_BETA1-3 : angle 1.48208 ( 3) link_BETA1-4 : bond 0.00263 ( 7) link_BETA1-4 : angle 1.59798 ( 21) link_BETA1-6 : bond 0.01579 ( 1) link_BETA1-6 : angle 3.43619 ( 3) link_NAG-ASN : bond 0.00378 ( 12) link_NAG-ASN : angle 2.41777 ( 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 146 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.393 Fit side-chains REVERT: A 99 GLU cc_start: 0.8204 (tp30) cc_final: 0.7999 (tt0) REVERT: A 253 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8306 (t70) REVERT: A 343 MET cc_start: 0.9068 (tpp) cc_final: 0.8671 (tpp) REVERT: A 693 LYS cc_start: 0.9029 (mmtp) cc_final: 0.8770 (mmtp) REVERT: A 699 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7488 (pp) REVERT: B 80 LYS cc_start: 0.8490 (tttt) cc_final: 0.8053 (tppt) REVERT: B 169 SER cc_start: 0.9120 (t) cc_final: 0.8620 (p) REVERT: B 241 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7104 (mp) REVERT: B 280 GLU cc_start: 0.6191 (pt0) cc_final: 0.5971 (pt0) REVERT: C 140 ASP cc_start: 0.8654 (m-30) cc_final: 0.8451 (m-30) REVERT: C 230 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8363 (mm) REVERT: C 237 ARG cc_start: 0.7010 (mtt180) cc_final: 0.6767 (mtt-85) REVERT: D 59 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7252 (mtp180) REVERT: D 80 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8204 (mp) REVERT: D 91 TYR cc_start: 0.7961 (m-80) cc_final: 0.7699 (m-80) outliers start: 35 outliers final: 21 residues processed: 138 average time/residue: 0.1070 time to fit residues: 20.9321 Evaluate side-chains 138 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 127 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 38 optimal weight: 0.0070 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102675 restraints weight = 14009.458| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.92 r_work: 0.2948 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11158 Z= 0.126 Angle : 0.597 12.827 15256 Z= 0.285 Chirality : 0.043 0.244 1813 Planarity : 0.004 0.039 1833 Dihedral : 8.694 77.278 2123 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.66 % Allowed : 11.99 % Favored : 85.35 % 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: 0.24 (0.24), residues: 1303 helix: 1.71 (0.20), residues: 713 sheet: -1.06 (0.42), residues: 130 loop : -2.05 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 391 TYR 0.014 0.001 TYR A 569 PHE 0.030 0.001 PHE A 302 TRP 0.008 0.001 TRP C 209 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00295 (11133) covalent geometry : angle 0.58212 (15185) SS BOND : bond 0.00259 ( 4) SS BOND : angle 0.69006 ( 8) hydrogen bonds : bond 0.03941 ( 545) hydrogen bonds : angle 3.76569 ( 1587) link_BETA1-3 : bond 0.00642 ( 1) link_BETA1-3 : angle 1.61765 ( 3) link_BETA1-4 : bond 0.00278 ( 7) link_BETA1-4 : angle 1.56323 ( 21) link_BETA1-6 : bond 0.01507 ( 1) link_BETA1-6 : angle 3.42543 ( 3) link_NAG-ASN : bond 0.00368 ( 12) link_NAG-ASN : angle 2.27501 ( 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 144 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.313 Fit side-chains REVERT: A 99 GLU cc_start: 0.8236 (tp30) cc_final: 0.8019 (tt0) REVERT: A 253 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8313 (t70) REVERT: A 693 LYS cc_start: 0.9014 (mmtp) cc_final: 0.8739 (mmtp) REVERT: A 699 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7450 (pp) REVERT: B 80 LYS cc_start: 0.8556 (tttt) cc_final: 0.8078 (tppt) REVERT: B 163 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.6969 (t-90) REVERT: B 169 SER cc_start: 0.9100 (t) cc_final: 0.8596 (p) REVERT: B 241 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7110 (mp) REVERT: B 280 GLU cc_start: 0.6189 (pt0) cc_final: 0.5826 (pt0) REVERT: C 230 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8330 (mm) REVERT: C 237 ARG cc_start: 0.6944 (mtt180) cc_final: 0.6666 (mtt-85) REVERT: D 59 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7258 (mtp180) REVERT: D 80 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8204 (mp) REVERT: D 91 TYR cc_start: 0.7971 (m-80) cc_final: 0.7707 (m-80) outliers start: 30 outliers final: 20 residues processed: 138 average time/residue: 0.1086 time to fit residues: 21.2103 Evaluate side-chains 138 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 17 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 2 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 overall best weight: 0.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN B 135 ASN D 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.134826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.108006 restraints weight = 13978.703| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.99 r_work: 0.3001 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11158 Z= 0.093 Angle : 0.544 11.785 15256 Z= 0.261 Chirality : 0.041 0.242 1813 Planarity : 0.003 0.039 1833 Dihedral : 7.969 75.491 2123 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.87 % Allowed : 13.23 % Favored : 84.90 % 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: 0.60 (0.24), residues: 1303 helix: 1.96 (0.20), residues: 716 sheet: -0.82 (0.43), residues: 129 loop : -1.86 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 391 TYR 0.012 0.001 TYR A 94 PHE 0.030 0.001 PHE A 302 TRP 0.007 0.001 TRP C 209 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00197 (11133) covalent geometry : angle 0.53185 (15185) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.56305 ( 8) hydrogen bonds : bond 0.03267 ( 545) hydrogen bonds : angle 3.61503 ( 1587) link_BETA1-3 : bond 0.00749 ( 1) link_BETA1-3 : angle 0.93886 ( 3) link_BETA1-4 : bond 0.00439 ( 7) link_BETA1-4 : angle 1.35704 ( 21) link_BETA1-6 : bond 0.00989 ( 1) link_BETA1-6 : angle 3.15232 ( 3) link_NAG-ASN : bond 0.00368 ( 12) link_NAG-ASN : angle 1.97440 ( 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 152 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8209 (tp30) cc_final: 0.7985 (tt0) REVERT: A 143 ASP cc_start: 0.8351 (t0) cc_final: 0.8092 (t0) REVERT: A 699 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7418 (pp) REVERT: B 80 LYS cc_start: 0.8328 (tttt) cc_final: 0.7861 (tppt) REVERT: B 163 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.6904 (t-90) REVERT: B 169 SER cc_start: 0.9042 (t) cc_final: 0.8570 (p) REVERT: B 241 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6634 (mp) REVERT: B 280 GLU cc_start: 0.6023 (pt0) cc_final: 0.5647 (pt0) REVERT: C 10 THR cc_start: 0.9033 (t) cc_final: 0.8695 (p) REVERT: C 237 ARG cc_start: 0.6897 (mtt180) cc_final: 0.6631 (mtt-85) REVERT: D 59 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7191 (mtt180) REVERT: D 80 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8052 (mp) REVERT: D 91 TYR cc_start: 0.7975 (m-80) cc_final: 0.7712 (m-80) outliers start: 21 outliers final: 10 residues processed: 147 average time/residue: 0.1061 time to fit residues: 22.1667 Evaluate side-chains 131 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.133477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.107431 restraints weight = 13752.921| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.92 r_work: 0.2942 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11158 Z= 0.136 Angle : 0.607 13.219 15256 Z= 0.288 Chirality : 0.043 0.241 1813 Planarity : 0.004 0.036 1833 Dihedral : 8.012 76.628 2123 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.60 % Allowed : 13.68 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1303 helix: 1.92 (0.20), residues: 715 sheet: -0.78 (0.43), residues: 132 loop : -1.85 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 391 TYR 0.015 0.001 TYR A 569 PHE 0.029 0.001 PHE A 302 TRP 0.008 0.001 TRP A 257 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00322 (11133) covalent geometry : angle 0.59357 (15185) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.66018 ( 8) hydrogen bonds : bond 0.03958 ( 545) hydrogen bonds : angle 3.70008 ( 1587) link_BETA1-3 : bond 0.00607 ( 1) link_BETA1-3 : angle 1.59380 ( 3) link_BETA1-4 : bond 0.00229 ( 7) link_BETA1-4 : angle 1.54311 ( 21) link_BETA1-6 : bond 0.00962 ( 1) link_BETA1-6 : angle 2.84754 ( 3) link_NAG-ASN : bond 0.00353 ( 12) link_NAG-ASN : angle 2.22166 ( 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 135 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.401 Fit side-chains REVERT: A 99 GLU cc_start: 0.8207 (tp30) cc_final: 0.7986 (tt0) REVERT: A 143 ASP cc_start: 0.8539 (t0) cc_final: 0.8278 (t0) REVERT: A 343 MET cc_start: 0.9039 (tpp) cc_final: 0.8669 (tpp) REVERT: A 599 LEU cc_start: 0.8386 (mp) cc_final: 0.8149 (mt) REVERT: A 699 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7435 (pp) REVERT: B 80 LYS cc_start: 0.8556 (tttt) cc_final: 0.8061 (tppt) REVERT: B 163 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.6957 (t-90) REVERT: B 169 SER cc_start: 0.9084 (t) cc_final: 0.8558 (p) REVERT: B 241 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6817 (mp) REVERT: B 280 GLU cc_start: 0.6120 (pt0) cc_final: 0.5768 (pt0) REVERT: C 237 ARG cc_start: 0.6919 (mtt180) cc_final: 0.6662 (mtt-85) REVERT: D 59 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7203 (mtt180) REVERT: D 80 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8108 (mp) REVERT: D 91 TYR cc_start: 0.7973 (m-80) cc_final: 0.7701 (m-80) outliers start: 18 outliers final: 13 residues processed: 132 average time/residue: 0.1066 time to fit residues: 20.2160 Evaluate side-chains 132 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 40 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.130785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104099 restraints weight = 13863.956| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.97 r_work: 0.2938 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11158 Z= 0.136 Angle : 0.600 12.823 15256 Z= 0.286 Chirality : 0.043 0.239 1813 Planarity : 0.004 0.035 1833 Dihedral : 7.833 75.785 2123 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.69 % Allowed : 13.68 % Favored : 84.64 % 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: 0.56 (0.24), residues: 1303 helix: 1.90 (0.20), residues: 720 sheet: -0.86 (0.43), residues: 129 loop : -1.84 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 391 TYR 0.013 0.001 TYR A 569 PHE 0.029 0.001 PHE A 302 TRP 0.008 0.001 TRP D 58 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00325 (11133) covalent geometry : angle 0.58733 (15185) SS BOND : bond 0.00253 ( 4) SS BOND : angle 0.62177 ( 8) hydrogen bonds : bond 0.03960 ( 545) hydrogen bonds : angle 3.71679 ( 1587) link_BETA1-3 : bond 0.00747 ( 1) link_BETA1-3 : angle 1.42310 ( 3) link_BETA1-4 : bond 0.00266 ( 7) link_BETA1-4 : angle 1.58704 ( 21) link_BETA1-6 : bond 0.00944 ( 1) link_BETA1-6 : angle 2.48249 ( 3) link_NAG-ASN : bond 0.00357 ( 12) link_NAG-ASN : angle 2.24504 ( 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 133 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.374 Fit side-chains REVERT: A 99 GLU cc_start: 0.8207 (tp30) cc_final: 0.7979 (tt0) REVERT: A 599 LEU cc_start: 0.8380 (mp) cc_final: 0.8169 (mt) REVERT: A 699 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7403 (pp) REVERT: B 80 LYS cc_start: 0.8352 (tttt) cc_final: 0.7853 (tppt) REVERT: B 163 HIS cc_start: 0.7421 (OUTLIER) cc_final: 0.6913 (t-90) REVERT: B 169 SER cc_start: 0.9120 (t) cc_final: 0.8593 (p) REVERT: B 210 MET cc_start: 0.8789 (mmp) cc_final: 0.8514 (mmp) REVERT: B 241 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6793 (mp) REVERT: B 280 GLU cc_start: 0.6173 (pt0) cc_final: 0.5836 (pt0) REVERT: C 237 ARG cc_start: 0.6926 (mtt180) cc_final: 0.6674 (mtt-85) REVERT: D 59 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7209 (mtt180) REVERT: D 80 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8144 (mp) REVERT: D 91 TYR cc_start: 0.7923 (m-80) cc_final: 0.7646 (m-80) outliers start: 19 outliers final: 14 residues processed: 131 average time/residue: 0.1052 time to fit residues: 19.5121 Evaluate side-chains 130 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 83 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.135454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.110760 restraints weight = 13613.459| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.85 r_work: 0.2951 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11158 Z= 0.147 Angle : 0.617 13.044 15256 Z= 0.294 Chirality : 0.044 0.241 1813 Planarity : 0.004 0.035 1833 Dihedral : 7.734 75.544 2123 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.95 % Allowed : 13.50 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1303 helix: 1.87 (0.20), residues: 719 sheet: -0.87 (0.42), residues: 130 loop : -1.87 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 391 TYR 0.015 0.001 TYR A 569 PHE 0.030 0.001 PHE A 302 TRP 0.009 0.001 TRP D 58 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00354 (11133) covalent geometry : angle 0.60438 (15185) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.67711 ( 8) hydrogen bonds : bond 0.04143 ( 545) hydrogen bonds : angle 3.75250 ( 1587) link_BETA1-3 : bond 0.00716 ( 1) link_BETA1-3 : angle 1.58636 ( 3) link_BETA1-4 : bond 0.00241 ( 7) link_BETA1-4 : angle 1.65351 ( 21) link_BETA1-6 : bond 0.00846 ( 1) link_BETA1-6 : angle 2.04503 ( 3) link_NAG-ASN : bond 0.00370 ( 12) link_NAG-ASN : angle 2.28044 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.45 seconds wall clock time: 45 minutes 22.28 seconds (2722.28 seconds total)