Starting phenix.real_space_refine on Fri Sep 11 20:50:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c9i_30312/09_2026/7c9i_30312.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c9i_30312/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7c9i_30312/09_2026/7c9i_30312.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c9i_30312/09_2026/7c9i_30312.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c9i_30312/09_2026/7c9i_30312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c9i_30312/09_2026/7c9i_30312.map" model { file = "/net/cci-nas-00/data/ceres_data/7c9i_30312/09_2026/7c9i_30312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c9i_30312/09_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): 0.14s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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: 2.40, per 1000 atoms: 0.22 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: 1.00 Conformation dependent library (CDL) restraints added in 517.4 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: 1.74 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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 - 16.29: 5960 16.29 - 32.58: 244 32.58 - 48.87: 69 48.87 - 65.16: 10 65.16 - 81.45: 9 Dihedral angle restraints: 6292 sinusoidal: 2459 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 6289 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: 3.440 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.970 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 10.619 75.505 3810 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/Z covalent geometry : bond 0.00788 / 0.35 (11133) covalent geometry : angle 1.06473 / 0.54 (15185) SS BOND : bond 0.00526 / 0.27 ( 4) SS BOND : angle 2.15415 / 1.43 ( 8) hydrogen bonds : bond 0.18515 / 12.44 ( 545) hydrogen bonds : angle 6.91153 / 4.68 ( 1587) link_BETA1-3 : bond 0.00062 / 0.03 ( 1) link_BETA1-3 : angle 1.42955 / 0.83 ( 3) link_BETA1-4 : bond 0.00603 / 0.30 ( 7) link_BETA1-4 : angle 2.60600 / 1.73 ( 21) link_BETA1-6 : bond 0.00405 / 0.21 ( 1) link_BETA1-6 : angle 1.49457 / 1.22 ( 3) link_NAG-ASN : bond 0.01070 / 0.59 ( 12) link_NAG-ASN : angle 5.05670 / 3.84 ( 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 : 0.406 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: 0.1225 time to fit residues: 33.3121 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 : 0.380 ------------------------------------------------------------------------------- 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... 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 = 0.3564 r_free = 0.3564 target = 0.137570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.112887 restraints weight = 13645.457| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.83 r_work: 0.2980 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11158 Z= 0.154 Angle : 0.688 12.237 15256 Z= 0.335 Chirality : 0.045 0.264 1813 Planarity : 0.005 0.049 1833 Dihedral : 6.991 82.753 1506 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.59 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: -1.88 (0.21), residues: 1303 helix: -0.15 (0.19), residues: 711 sheet: -1.75 (0.40), residues: 122 loop : -2.78 (0.23), residues: 470 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 0.020 0.002 TRP C 209 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (11133) covalent geometry : angle 0.66431 / 0.33 (15185) SS BOND : bond 0.00614 / 0.31 ( 4) SS BOND : angle 1.07445 / 0.63 ( 8) hydrogen bonds : bond 0.05394 / 3.56 ( 545) hydrogen bonds : angle 4.48801 / 3.01 ( 1587) link_BETA1-3 : bond 0.00353 / 0.19 ( 1) link_BETA1-3 : angle 1.93949 / 1.54 ( 3) link_BETA1-4 : bond 0.00542 / 0.28 ( 7) link_BETA1-4 : angle 1.68816 / 1.05 ( 21) link_BETA1-6 : bond 0.01227 / 0.65 ( 1) link_BETA1-6 : angle 1.47493 / 1.06 ( 3) link_NAG-ASN : bond 0.00541 / 0.30 ( 12) link_NAG-ASN : angle 3.42820 / 2.80 ( 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 : 0.401 Fit side-chains REVERT: A 99 GLU cc_start: 0.8309 (tp30) cc_final: 0.8106 (tt0) REVERT: A 237 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7521 (mm-40) REVERT: A 246 ILE cc_start: 0.8525 (mm) cc_final: 0.8284 (mt) REVERT: A 343 MET cc_start: 0.9078 (tpp) cc_final: 0.8677 (tpp) REVERT: A 474 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7702 (tm-30) REVERT: A 636 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 693 LYS cc_start: 0.8831 (mmtp) cc_final: 0.8587 (mmtp) REVERT: B 80 LYS cc_start: 0.8583 (tttt) cc_final: 0.8064 (tppt) REVERT: B 165 TRP cc_start: 0.7662 (t60) cc_final: 0.7076 (t60) REVERT: B 169 SER cc_start: 0.9179 (t) cc_final: 0.8651 (p) REVERT: B 210 MET cc_start: 0.9049 (mmt) cc_final: 0.8371 (mmt) REVERT: C 140 ASP cc_start: 0.8522 (m-30) cc_final: 0.8311 (m-30) REVERT: C 237 ARG cc_start: 0.7049 (mtt180) cc_final: 0.6779 (mtt-85) REVERT: D 8 ASN cc_start: 0.7661 (m110) cc_final: 0.7384 (m-40) REVERT: D 34 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8193 (mp) REVERT: D 54 LYS cc_start: 0.7372 (ttpt) cc_final: 0.7003 (ttpp) REVERT: D 91 TYR cc_start: 0.7965 (m-80) cc_final: 0.7522 (m-80) outliers start: 18 outliers final: 12 residues processed: 149 average time/residue: 0.1116 time to fit residues: 23.2364 Evaluate side-chains 133 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 686 VAL 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: 4.9990 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: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3434 r_free = 0.3434 target = 0.128388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.101345 restraints weight = 14100.079| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.95 r_work: 0.2919 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11158 Z= 0.195 Angle : 0.693 14.006 15256 Z= 0.334 Chirality : 0.046 0.246 1813 Planarity : 0.005 0.044 1833 Dihedral : 6.944 81.135 1502 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % 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: -0.97 (0.23), residues: 1303 helix: 0.70 (0.20), residues: 707 sheet: -1.62 (0.40), residues: 126 loop : -2.49 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 391 TYR 0.016 0.002 TYR A 569 PHE 0.035 0.002 PHE A 302 TRP 0.018 0.002 TRP C 209 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (11133) covalent geometry : angle 0.67289 / 0.33 (15185) SS BOND : bond 0.00348 / 0.18 ( 4) SS BOND : angle 1.08117 / 0.69 ( 8) hydrogen bonds : bond 0.05181 / 3.41 ( 545) hydrogen bonds : angle 4.17725 / 2.78 ( 1587) link_BETA1-3 : bond 0.00186 / 0.10 ( 1) link_BETA1-3 : angle 1.54585 / 1.10 ( 3) link_BETA1-4 : bond 0.00367 / 0.19 ( 7) link_BETA1-4 : angle 1.75731 / 1.08 ( 21) link_BETA1-6 : bond 0.00977 / 0.51 ( 1) link_BETA1-6 : angle 1.38865 / 0.97 ( 3) link_NAG-ASN : bond 0.00442 / 0.24 ( 12) link_NAG-ASN : angle 3.13454 / 2.61 ( 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 146 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.448 Fit side-chains REVERT: A 99 GLU cc_start: 0.8368 (tp30) cc_final: 0.8109 (tt0) REVERT: A 343 MET cc_start: 0.9074 (tpp) cc_final: 0.8741 (tpp) REVERT: A 474 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7862 (tm-30) REVERT: A 693 LYS cc_start: 0.8911 (mmtp) cc_final: 0.8640 (mmtp) REVERT: A 699 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7403 (pp) REVERT: B 80 LYS cc_start: 0.8604 (tttt) cc_final: 0.8099 (tppt) REVERT: B 159 TYR cc_start: 0.6306 (m-80) cc_final: 0.5966 (m-80) REVERT: B 169 SER cc_start: 0.9169 (t) cc_final: 0.8627 (p) REVERT: B 210 MET cc_start: 0.8946 (mmt) cc_final: 0.8431 (mmt) REVERT: B 280 GLU cc_start: 0.6454 (pt0) cc_final: 0.6095 (pt0) REVERT: C 140 ASP cc_start: 0.8645 (m-30) cc_final: 0.8436 (m-30) REVERT: C 237 ARG cc_start: 0.7057 (mtt180) cc_final: 0.6740 (mtt-85) REVERT: D 34 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8237 (mp) REVERT: D 91 TYR cc_start: 0.8088 (m-80) cc_final: 0.7654 (m-80) outliers start: 29 outliers final: 17 residues processed: 138 average time/residue: 0.1151 time to fit residues: 22.1983 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 : 0.446 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 39 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 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: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3399 r_free = 0.3399 target = 0.126101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.099190 restraints weight = 14153.454| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.93 r_work: 0.2893 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11158 Z= 0.194 Angle : 0.683 14.000 15256 Z= 0.329 Chirality : 0.046 0.247 1813 Planarity : 0.004 0.041 1833 Dihedral : 7.028 79.113 1502 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.58 % Allowed : 10.66 % Favored : 86.77 % 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 (0.23), residues: 1303 helix: 1.01 (0.20), residues: 710 sheet: -1.51 (0.42), residues: 119 loop : -2.33 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 391 TYR 0.016 0.002 TYR A 569 PHE 0.033 0.002 PHE A 302 TRP 0.012 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.19 (11133) covalent geometry : angle 0.66373 / 0.32 (15185) SS BOND : bond 0.00311 / 0.16 ( 4) SS BOND : angle 1.08730 / 0.63 ( 8) hydrogen bonds : bond 0.04910 / 3.22 ( 545) hydrogen bonds : angle 4.11202 / 2.74 ( 1587) link_BETA1-3 : bond 0.00239 / 0.13 ( 1) link_BETA1-3 : angle 1.47869 / 1.09 ( 3) link_BETA1-4 : bond 0.00321 / 0.16 ( 7) link_BETA1-4 : angle 1.74133 / 1.05 ( 21) link_BETA1-6 : bond 0.01009 / 0.53 ( 1) link_BETA1-6 : angle 1.49837 / 1.08 ( 3) link_NAG-ASN : bond 0.00427 / 0.23 ( 12) link_NAG-ASN : angle 3.07259 / 2.56 ( 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 143 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.389 Fit side-chains REVERT: A 99 GLU cc_start: 0.8326 (tp30) cc_final: 0.8073 (tt0) REVERT: A 160 ARG cc_start: 0.8769 (ptp-170) cc_final: 0.8547 (ptp-170) REVERT: A 343 MET cc_start: 0.9092 (tpp) cc_final: 0.8713 (tpp) REVERT: A 693 LYS cc_start: 0.9014 (mmtp) cc_final: 0.8754 (mmtp) REVERT: A 699 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7457 (pp) REVERT: B 80 LYS cc_start: 0.8537 (tttt) cc_final: 0.8043 (tppt) REVERT: B 159 TYR cc_start: 0.6429 (m-80) cc_final: 0.6136 (m-80) REVERT: B 169 SER cc_start: 0.9181 (t) cc_final: 0.8662 (p) REVERT: B 241 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7263 (mp) REVERT: B 280 GLU cc_start: 0.6414 (pt0) cc_final: 0.6033 (pt0) REVERT: C 138 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8269 (mp) REVERT: C 140 ASP cc_start: 0.8668 (m-30) cc_final: 0.8463 (m-30) REVERT: C 214 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7994 (mp) REVERT: C 237 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6772 (mtt-85) REVERT: D 34 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8225 (mp) REVERT: D 80 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8196 (mp) REVERT: D 91 TYR cc_start: 0.7998 (m-80) cc_final: 0.7517 (m-80) outliers start: 29 outliers final: 20 residues processed: 136 average time/residue: 0.1149 time to fit residues: 22.0690 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 : 0.437 ------------------------------------------------------------------------------- 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 241 LEU Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 406 THR 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 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 34 ILE Chi-restraints excluded: chain D residue 48 THR 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: 0.0010 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3570 r_free = 0.3570 target = 0.137892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113434 restraints weight = 13592.508| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.80 r_work: 0.2955 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11158 Z= 0.120 Angle : 0.590 12.431 15256 Z= 0.286 Chirality : 0.042 0.247 1813 Planarity : 0.004 0.040 1833 Dihedral : 6.627 76.898 1502 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.02 % Allowed : 11.10 % Favored : 85.88 % 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: -0.15 (0.24), residues: 1303 helix: 1.39 (0.20), residues: 713 sheet: -1.24 (0.41), residues: 130 loop : -2.20 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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/Z covalent geometry : bond 0.00280 / 0.12 (11133) covalent geometry : angle 0.57561 / 0.28 (15185) SS BOND : bond 0.00279 / 0.14 ( 4) SS BOND : angle 0.71678 / 0.49 ( 8) hydrogen bonds : bond 0.04028 / 2.64 ( 545) hydrogen bonds : angle 3.90521 / 2.61 ( 1587) link_BETA1-3 : bond 0.00356 / 0.19 ( 1) link_BETA1-3 : angle 1.43404 / 1.10 ( 3) link_BETA1-4 : bond 0.00375 / 0.19 ( 7) link_BETA1-4 : angle 1.46171 / 0.88 ( 21) link_BETA1-6 : bond 0.00894 / 0.47 ( 1) link_BETA1-6 : angle 1.53908 / 1.11 ( 3) link_NAG-ASN : bond 0.00379 / 0.20 ( 12) link_NAG-ASN : angle 2.49110 / 2.10 ( 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 155 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.423 Fit side-chains REVERT: A 99 GLU cc_start: 0.8210 (tp30) cc_final: 0.7979 (tt0) REVERT: A 215 MET cc_start: 0.9219 (ttm) cc_final: 0.9002 (ttp) REVERT: A 693 LYS cc_start: 0.8991 (mmtp) cc_final: 0.8718 (mmtp) REVERT: A 699 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7394 (pp) REVERT: B 80 LYS cc_start: 0.8555 (tttt) cc_final: 0.8082 (tppt) REVERT: B 169 SER cc_start: 0.9107 (t) cc_final: 0.8605 (p) REVERT: B 241 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7126 (mp) REVERT: B 280 GLU cc_start: 0.6167 (pt0) cc_final: 0.5790 (pt0) REVERT: C 140 ASP cc_start: 0.8565 (m-30) cc_final: 0.8358 (m-30) REVERT: C 230 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8327 (mm) REVERT: C 237 ARG cc_start: 0.6998 (mtt180) cc_final: 0.6791 (mtt-85) REVERT: D 80 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8128 (mp) REVERT: D 91 TYR cc_start: 0.7875 (m-80) cc_final: 0.7562 (m-80) outliers start: 34 outliers final: 18 residues processed: 147 average time/residue: 0.1089 time to fit residues: 22.7199 Evaluate side-chains 136 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL 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 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 270 MET 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 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: 0.9980 chunk 66 optimal weight: 4.9990 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: 0.9980 chunk 9 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.099694 restraints weight = 14113.893| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.92 r_work: 0.2908 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11158 Z= 0.180 Angle : 0.656 13.209 15256 Z= 0.314 Chirality : 0.045 0.253 1813 Planarity : 0.004 0.040 1833 Dihedral : 6.794 77.587 1502 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.84 % Allowed : 11.46 % 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: -0.12 (0.24), residues: 1303 helix: 1.40 (0.20), residues: 713 sheet: -1.16 (0.42), residues: 130 loop : -2.17 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 391 TYR 0.016 0.002 TYR A 569 PHE 0.031 0.002 PHE A 302 TRP 0.010 0.001 TRP A 257 HIS 0.004 0.001 HIS C 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (11133) covalent geometry : angle 0.63981 / 0.31 (15185) SS BOND : bond 0.00276 / 0.14 ( 4) SS BOND : angle 0.86243 / 0.52 ( 8) hydrogen bonds : bond 0.04606 / 3.03 ( 545) hydrogen bonds : angle 3.94322 / 2.62 ( 1587) link_BETA1-3 : bond 0.00250 / 0.13 ( 1) link_BETA1-3 : angle 1.34838 / 1.00 ( 3) link_BETA1-4 : bond 0.00293 / 0.15 ( 7) link_BETA1-4 : angle 1.64441 / 1.01 ( 21) link_BETA1-6 : bond 0.00854 / 0.45 ( 1) link_BETA1-6 : angle 1.45971 / 1.07 ( 3) link_NAG-ASN : bond 0.00366 / 0.19 ( 12) link_NAG-ASN : angle 2.80653 / 2.32 ( 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 143 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.409 Fit side-chains REVERT: A 99 GLU cc_start: 0.8280 (tp30) cc_final: 0.8058 (tt0) REVERT: A 343 MET cc_start: 0.9095 (tpp) cc_final: 0.8727 (tpp) REVERT: A 693 LYS cc_start: 0.9030 (mmtp) cc_final: 0.8757 (mmtp) REVERT: A 699 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7460 (pp) REVERT: B 80 LYS cc_start: 0.8525 (tttt) cc_final: 0.8037 (tppt) REVERT: B 163 HIS cc_start: 0.7617 (OUTLIER) cc_final: 0.7024 (t-90) REVERT: B 169 SER cc_start: 0.9129 (t) cc_final: 0.8575 (p) REVERT: B 241 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7243 (mp) REVERT: B 280 GLU cc_start: 0.6351 (pt0) cc_final: 0.6009 (pt0) REVERT: C 140 ASP cc_start: 0.8650 (m-30) cc_final: 0.8435 (m-30) REVERT: C 237 ARG cc_start: 0.7035 (mtt180) cc_final: 0.6748 (mtt-85) REVERT: D 80 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8178 (mp) REVERT: D 91 TYR cc_start: 0.7925 (m-80) cc_final: 0.7645 (m-80) outliers start: 32 outliers final: 21 residues processed: 138 average time/residue: 0.1139 time to fit residues: 22.1508 Evaluate side-chains 136 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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 287 ILE 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 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=2.50 ------------------------------------------------------------------------------- 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: 0.0970 chunk 35 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 135 ASN D 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.102254 restraints weight = 13966.557| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.92 r_work: 0.2947 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11158 Z= 0.121 Angle : 0.596 12.349 15256 Z= 0.286 Chirality : 0.042 0.249 1813 Planarity : 0.004 0.040 1833 Dihedral : 6.556 75.647 1502 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.58 % Allowed : 12.43 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.24), residues: 1303 helix: 1.62 (0.20), residues: 713 sheet: -1.12 (0.42), residues: 130 loop : -2.07 (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/Z covalent geometry : bond 0.00278 / 0.12 (11133) covalent geometry : angle 0.58195 / 0.28 (15185) SS BOND : bond 0.00259 / 0.13 ( 4) SS BOND : angle 0.64451 / 0.45 ( 8) hydrogen bonds : bond 0.04003 / 2.63 ( 545) hydrogen bonds : angle 3.82260 / 2.55 ( 1587) link_BETA1-3 : bond 0.00306 / 0.16 ( 1) link_BETA1-3 : angle 1.32863 / 1.02 ( 3) link_BETA1-4 : bond 0.00351 / 0.18 ( 7) link_BETA1-4 : angle 1.45203 / 0.89 ( 21) link_BETA1-6 : bond 0.00891 / 0.47 ( 1) link_BETA1-6 : angle 1.54394 / 1.13 ( 3) link_NAG-ASN : bond 0.00350 / 0.19 ( 12) link_NAG-ASN : angle 2.44738 / 2.05 ( 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 141 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.409 Fit side-chains REVERT: A 99 GLU cc_start: 0.8261 (tp30) cc_final: 0.8040 (tt0) REVERT: A 699 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7468 (pp) REVERT: B 80 LYS cc_start: 0.8509 (tttt) cc_final: 0.8049 (tppt) REVERT: B 163 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.6897 (t-90) REVERT: B 169 SER cc_start: 0.9112 (t) cc_final: 0.8589 (p) REVERT: B 241 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7112 (mp) REVERT: B 280 GLU cc_start: 0.6296 (pt0) cc_final: 0.5930 (pt0) REVERT: C 230 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8333 (mm) REVERT: C 237 ARG cc_start: 0.6991 (mtt180) cc_final: 0.6716 (mtt-85) REVERT: D 59 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7285 (mtp180) REVERT: D 80 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8140 (mp) REVERT: D 91 TYR cc_start: 0.7982 (m-80) cc_final: 0.7691 (m-80) outliers start: 29 outliers final: 21 residues processed: 136 average time/residue: 0.1115 time to fit residues: 21.6111 Evaluate side-chains 135 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 605 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 114 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 17 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 2 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN B 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105211 restraints weight = 14010.894| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.92 r_work: 0.3017 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11158 Z= 0.101 Angle : 0.559 11.697 15256 Z= 0.269 Chirality : 0.041 0.250 1813 Planarity : 0.004 0.040 1833 Dihedral : 6.278 74.838 1502 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.49 % Allowed : 12.43 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1303 helix: 1.83 (0.20), residues: 714 sheet: -0.91 (0.43), residues: 132 loop : -1.93 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 391 TYR 0.013 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/Z covalent geometry : bond 0.00224 / 0.10 (11133) covalent geometry : angle 0.54635 / 0.27 (15185) SS BOND : bond 0.00255 / 0.13 ( 4) SS BOND : angle 0.62209 / 0.46 ( 8) hydrogen bonds : bond 0.03564 / 2.34 ( 545) hydrogen bonds : angle 3.69933 / 2.47 ( 1587) link_BETA1-3 : bond 0.00333 / 0.18 ( 1) link_BETA1-3 : angle 1.37044 / 1.06 ( 3) link_BETA1-4 : bond 0.00367 / 0.18 ( 7) link_BETA1-4 : angle 1.29449 / 0.81 ( 21) link_BETA1-6 : bond 0.00823 / 0.43 ( 1) link_BETA1-6 : angle 1.53473 / 1.13 ( 3) link_NAG-ASN : bond 0.00334 / 0.18 ( 12) link_NAG-ASN : angle 2.21264 / 1.81 ( 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 154 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8196 (tp30) cc_final: 0.7994 (tt0) REVERT: A 215 MET cc_start: 0.9292 (ttm) cc_final: 0.9033 (ttp) REVERT: A 599 LEU cc_start: 0.8474 (mp) cc_final: 0.8213 (mt) REVERT: A 699 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7486 (pp) REVERT: B 80 LYS cc_start: 0.8499 (tttt) cc_final: 0.8052 (tppt) REVERT: B 163 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.6920 (t-90) REVERT: B 169 SER cc_start: 0.9101 (t) cc_final: 0.8623 (p) REVERT: B 241 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6914 (mp) REVERT: C 10 THR cc_start: 0.9081 (t) cc_final: 0.8774 (p) REVERT: C 237 ARG cc_start: 0.6970 (mtt180) cc_final: 0.6664 (mtt-85) REVERT: D 59 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7251 (mtt180) REVERT: D 80 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8107 (mp) REVERT: D 91 TYR cc_start: 0.8001 (m-80) cc_final: 0.7717 (m-80) outliers start: 28 outliers final: 19 residues processed: 150 average time/residue: 0.1103 time to fit residues: 23.7306 Evaluate side-chains 141 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 512 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.103256 restraints weight = 13934.780| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.91 r_work: 0.2944 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2670 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= 0.127 Angle : 0.589 12.617 15256 Z= 0.283 Chirality : 0.043 0.251 1813 Planarity : 0.004 0.084 1833 Dihedral : 6.339 75.184 1502 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.58 % Allowed : 12.97 % Favored : 84.46 % 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: 0.45 (0.24), residues: 1303 helix: 1.83 (0.20), residues: 718 sheet: -0.85 (0.43), residues: 133 loop : -1.94 (0.28), residues: 452 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 0.029 0.001 PHE A 302 TRP 0.007 0.001 TRP D 58 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (11133) covalent geometry : angle 0.57664 / 0.28 (15185) SS BOND : bond 0.00247 / 0.12 ( 4) SS BOND : angle 0.64971 / 0.42 ( 8) hydrogen bonds : bond 0.03901 / 2.56 ( 545) hydrogen bonds : angle 3.73214 / 2.49 ( 1587) link_BETA1-3 : bond 0.00277 / 0.15 ( 1) link_BETA1-3 : angle 1.31432 / 1.00 ( 3) link_BETA1-4 : bond 0.00329 / 0.17 ( 7) link_BETA1-4 : angle 1.39865 / 0.88 ( 21) link_BETA1-6 : bond 0.00890 / 0.47 ( 1) link_BETA1-6 : angle 1.55661 / 1.15 ( 3) link_NAG-ASN : bond 0.00326 / 0.17 ( 12) link_NAG-ASN : angle 2.30442 / 1.91 ( 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 145 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8221 (tp30) cc_final: 0.8011 (tt0) REVERT: A 599 LEU cc_start: 0.8490 (mp) cc_final: 0.8234 (mt) REVERT: A 699 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7465 (pp) REVERT: B 80 LYS cc_start: 0.8548 (tttt) cc_final: 0.8072 (tppt) REVERT: B 163 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.6922 (t-90) REVERT: B 169 SER cc_start: 0.9097 (t) cc_final: 0.8583 (p) REVERT: B 241 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6779 (mp) REVERT: B 273 GLU cc_start: 0.7445 (tt0) cc_final: 0.7190 (tt0) REVERT: C 237 ARG cc_start: 0.6897 (mtt180) cc_final: 0.6610 (mtt-85) REVERT: D 59 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7312 (mtt180) REVERT: D 80 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8112 (mp) REVERT: D 91 TYR cc_start: 0.7967 (m-80) cc_final: 0.7681 (m-80) outliers start: 29 outliers final: 23 residues processed: 141 average time/residue: 0.1075 time to fit residues: 21.4093 Evaluate side-chains 141 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 605 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 114 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 40 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 512 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106529 restraints weight = 13715.634| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.91 r_work: 0.2932 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2683 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= 0.143 Angle : 0.613 12.722 15256 Z= 0.293 Chirality : 0.043 0.248 1813 Planarity : 0.004 0.082 1833 Dihedral : 6.418 75.047 1502 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.40 % Allowed : 13.14 % Favored : 84.46 % 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: 0.39 (0.24), residues: 1303 helix: 1.77 (0.20), residues: 719 sheet: -0.95 (0.42), residues: 131 loop : -1.92 (0.28), residues: 453 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 A 257 HIS 0.003 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (11133) covalent geometry : angle 0.59950 / 0.29 (15185) SS BOND : bond 0.00228 / 0.11 ( 4) SS BOND : angle 0.64658 / 0.42 ( 8) hydrogen bonds : bond 0.04091 / 2.69 ( 545) hydrogen bonds : angle 3.76700 / 2.51 ( 1587) link_BETA1-3 : bond 0.00263 / 0.14 ( 1) link_BETA1-3 : angle 1.27989 / 0.97 ( 3) link_BETA1-4 : bond 0.00313 / 0.16 ( 7) link_BETA1-4 : angle 1.46169 / 0.91 ( 21) link_BETA1-6 : bond 0.00878 / 0.46 ( 1) link_BETA1-6 : angle 1.53004 / 1.14 ( 3) link_NAG-ASN : bond 0.00338 / 0.18 ( 12) link_NAG-ASN : angle 2.42082 / 2.00 ( 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 136 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.411 Fit side-chains REVERT: A 99 GLU cc_start: 0.8211 (tp30) cc_final: 0.7990 (tt0) REVERT: A 343 MET cc_start: 0.9040 (tpp) cc_final: 0.8684 (tpp) REVERT: A 599 LEU cc_start: 0.8484 (mp) cc_final: 0.8236 (mt) REVERT: A 699 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7448 (pp) REVERT: B 80 LYS cc_start: 0.8411 (tttt) cc_final: 0.7936 (tppt) REVERT: B 163 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6904 (t-90) REVERT: B 169 SER cc_start: 0.9134 (t) cc_final: 0.8603 (p) REVERT: B 210 MET cc_start: 0.8813 (mmp) cc_final: 0.8497 (mmp) REVERT: B 241 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6786 (mp) REVERT: C 237 ARG cc_start: 0.6913 (mtt180) cc_final: 0.6667 (mtt-85) REVERT: D 59 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7315 (mtt180) REVERT: D 80 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8107 (mp) REVERT: D 91 TYR cc_start: 0.7949 (m-80) cc_final: 0.7658 (m-80) outliers start: 27 outliers final: 22 residues processed: 133 average time/residue: 0.1056 time to fit residues: 19.7705 Evaluate side-chains 136 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL 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 483 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 605 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 114 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.102950 restraints weight = 13861.702| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.95 r_work: 0.2908 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11158 Z= 0.164 Angle : 0.641 13.157 15256 Z= 0.306 Chirality : 0.044 0.251 1813 Planarity : 0.004 0.080 1833 Dihedral : 6.604 74.772 1502 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.58 % Allowed : 13.14 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.24), residues: 1303 helix: 1.71 (0.20), residues: 719 sheet: -0.93 (0.42), residues: 130 loop : -1.92 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 391 TYR 0.015 0.001 TYR A 569 PHE 0.030 0.002 PHE A 302 TRP 0.009 0.001 TRP D 58 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (11133) covalent geometry : angle 0.62740 / 0.30 (15185) SS BOND : bond 0.00231 / 0.12 ( 4) SS BOND : angle 0.69447 / 0.44 ( 8) hydrogen bonds : bond 0.04392 / 2.90 ( 545) hydrogen bonds : angle 3.83064 / 2.56 ( 1587) link_BETA1-3 : bond 0.00224 / 0.12 ( 1) link_BETA1-3 : angle 1.22793 / 0.91 ( 3) link_BETA1-4 : bond 0.00312 / 0.16 ( 7) link_BETA1-4 : angle 1.56432 / 0.97 ( 21) link_BETA1-6 : bond 0.00883 / 0.46 ( 1) link_BETA1-6 : angle 1.51414 / 1.12 ( 3) link_NAG-ASN : bond 0.00355 / 0.19 ( 12) link_NAG-ASN : angle 2.54785 / 2.11 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2822.82 seconds wall clock time: 49 minutes 5.00 seconds (2945.00 seconds total)