Starting phenix.real_space_refine on Thu Mar 5 02:10:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6li9_0903/03_2026/6li9_0903.cif Found real_map, /net/cci-nas-00/data/ceres_data/6li9_0903/03_2026/6li9_0903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6li9_0903/03_2026/6li9_0903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6li9_0903/03_2026/6li9_0903.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6li9_0903/03_2026/6li9_0903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6li9_0903/03_2026/6li9_0903.map" } resolution = 2.3 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 90 5.16 5 C 11560 2.51 5 N 2832 2.21 5 O 3500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17988 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5084 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain: "B" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3538 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 26, 'TRANS': 431} Chain: "C" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5084 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain: "D" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3538 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 26, 'TRANS': 431} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Classifications: {'water': 116} Link IDs: {None: 115} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Classifications: {'water': 116} Link IDs: {None: 115} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 4.23, per 1000 atoms: 0.24 Number of scatterers: 17988 At special positions: 0 Unit cell: (81.825, 140.739, 138.557, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 90 16.00 P 4 15.00 O 3500 8.00 N 2832 7.00 C 11560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.04 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS D 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 273 " distance=2.04 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 666 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG E 1 " - " ASN A 261 " " NAG F 1 " - " ASN A 332 " " NAG G 1 " - " ASN A 495 " " NAG H 1 " - " ASN A 513 " " NAG I 1 " - " ASN A 575 " " NAG J 1 " - " ASN C 261 " " NAG K 1 " - " ASN C 332 " " NAG L 1 " - " ASN C 495 " " NAG M 1 " - " ASN C 513 " " NAG N 1 " - " ASN C 575 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 750.2 milliseconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4052 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 16 sheets defined 54.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.685A pdb=" N PHE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 111 removed outlier: 3.669A pdb=" N ILE A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 3.682A pdb=" N LEU A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.891A pdb=" N GLY A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.754A pdb=" N PHE A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.597A pdb=" N LYS A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.897A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.853A pdb=" N GLN A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 395 through 398 Processing helix chain 'A' and resid 420 through 435 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.728A pdb=" N SER A 505 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 530 through 535 removed outlier: 4.474A pdb=" N HIS A 534 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 547 through 562 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.663A pdb=" N LYS A 629 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'B' and resid 32 through 44 removed outlier: 3.648A pdb=" N SER B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.649A pdb=" N ASN B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 90 removed outlier: 3.946A pdb=" N GLY B 73 " --> pdb=" O TRP B 69 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 removed outlier: 3.611A pdb=" N ALA B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 removed outlier: 4.009A pdb=" N ALA B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 138 removed outlier: 3.855A pdb=" N TYR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 147 through 166 removed outlier: 3.738A pdb=" N ALA B 157 " --> pdb=" O CYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.532A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 201 removed outlier: 3.547A pdb=" N VAL B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 removed outlier: 3.536A pdb=" N PHE B 207 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP B 208 " --> pdb=" O LYS B 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 204 through 208' Processing helix chain 'B' and resid 219 through 231 removed outlier: 3.911A pdb=" N ALA B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.783A pdb=" N LEU B 238 " --> pdb=" O TRP B 235 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN B 239 " --> pdb=" O ASN B 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 239' Processing helix chain 'B' and resid 250 through 275 removed outlier: 3.526A pdb=" N ILE B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) Proline residue: B 261 - end of helix Processing helix chain 'B' and resid 279 through 285 removed outlier: 3.618A pdb=" N LEU B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 297 removed outlier: 3.598A pdb=" N ARG B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 321 removed outlier: 3.653A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.643A pdb=" N VAL B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 Processing helix chain 'B' and resid 373 through 396 removed outlier: 3.800A pdb=" N ALA B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 387 " --> pdb=" O TRP B 383 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 394 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 432 removed outlier: 3.512A pdb=" N VAL B 415 " --> pdb=" O VAL B 411 " (cutoff:3.500A) Proline residue: B 428 - end of helix Processing helix chain 'B' and resid 435 through 455 removed outlier: 3.621A pdb=" N VAL B 441 " --> pdb=" O TYR B 437 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 478 removed outlier: 3.504A pdb=" N SER B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS B 467 " --> pdb=" O GLN B 463 " (cutoff:3.500A) Proline residue: B 468 - end of helix Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.685A pdb=" N PHE C 74 " --> pdb=" O LYS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 111 removed outlier: 3.669A pdb=" N ILE C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 3.682A pdb=" N LEU C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 removed outlier: 3.891A pdb=" N GLY C 121 " --> pdb=" O TRP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 removed outlier: 3.754A pdb=" N PHE C 131 " --> pdb=" O PRO C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 189 through 203 removed outlier: 3.597A pdb=" N LYS C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 230 through 236 removed outlier: 3.897A pdb=" N THR C 234 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 306 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 356 through 370 removed outlier: 3.853A pdb=" N GLN C 370 " --> pdb=" O GLN C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 395 through 398 Processing helix chain 'C' and resid 420 through 435 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.728A pdb=" N SER C 505 " --> pdb=" O THR C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 519 Processing helix chain 'C' and resid 530 through 535 removed outlier: 4.474A pdb=" N HIS C 534 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 547 through 562 Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 606 through 610 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.663A pdb=" N LYS C 629 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'D' and resid 32 through 44 removed outlier: 3.648A pdb=" N SER D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 59 removed outlier: 3.649A pdb=" N ASN D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 90 removed outlier: 3.946A pdb=" N GLY D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.611A pdb=" N ALA D 103 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 119 removed outlier: 4.009A pdb=" N ALA D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 138 removed outlier: 3.855A pdb=" N TYR D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 147 through 166 removed outlier: 3.738A pdb=" N ALA D 157 " --> pdb=" O CYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.532A pdb=" N VAL D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 201 removed outlier: 3.547A pdb=" N VAL D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 208 removed outlier: 3.536A pdb=" N PHE D 207 " --> pdb=" O THR D 204 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP D 208 " --> pdb=" O LYS D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 204 through 208' Processing helix chain 'D' and resid 219 through 231 removed outlier: 3.911A pdb=" N ALA D 231 " --> pdb=" O ASN D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 removed outlier: 3.783A pdb=" N LEU D 238 " --> pdb=" O TRP D 235 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN D 239 " --> pdb=" O ASN D 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 235 through 239' Processing helix chain 'D' and resid 250 through 275 removed outlier: 3.526A pdb=" N ILE D 257 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Proline residue: D 261 - end of helix Processing helix chain 'D' and resid 279 through 285 removed outlier: 3.618A pdb=" N LEU D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 297 removed outlier: 3.598A pdb=" N ARG D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 321 removed outlier: 3.653A pdb=" N ALA D 310 " --> pdb=" O PRO D 306 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.643A pdb=" N VAL D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D 334 " --> pdb=" O VAL D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 366 Processing helix chain 'D' and resid 373 through 396 removed outlier: 3.800A pdb=" N ALA D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 387 " --> pdb=" O TRP D 383 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 389 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 394 " --> pdb=" O ILE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 432 removed outlier: 3.512A pdb=" N VAL D 415 " --> pdb=" O VAL D 411 " (cutoff:3.500A) Proline residue: D 428 - end of helix Processing helix chain 'D' and resid 435 through 455 removed outlier: 3.621A pdb=" N VAL D 441 " --> pdb=" O TYR D 437 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY D 447 " --> pdb=" O PHE D 443 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE D 450 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 478 removed outlier: 3.504A pdb=" N SER D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Proline residue: D 468 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 407 through 408 removed outlier: 4.050A pdb=" N PHE A 407 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 383 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP A 443 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N TYR A 479 " --> pdb=" O TRP A 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 7.266A pdb=" N LYS A 167 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.654A pdb=" N GLN A 272 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 330 removed outlier: 4.132A pdb=" N ILE A 329 " --> pdb=" O TYR A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 632 through 634 removed outlier: 11.292A pdb=" N LYS A 617 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ASN A 651 " --> pdb=" O LYS A 617 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ARG A 619 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 649 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE A 647 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER A 623 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY A 645 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 603 through 605 Processing sheet with id=AA7, first strand: chain 'A' and resid 673 through 675 Processing sheet with id=AA8, first strand: chain 'B' and resid 344 through 345 Processing sheet with id=AA9, first strand: chain 'C' and resid 407 through 408 removed outlier: 4.050A pdb=" N PHE C 407 " --> pdb=" O MET C 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 383 " --> pdb=" O PHE C 407 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP C 443 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N TYR C 479 " --> pdb=" O TRP C 443 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 168 removed outlier: 7.266A pdb=" N LYS C 167 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.654A pdb=" N GLN C 272 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 330 removed outlier: 4.132A pdb=" N ILE C 329 " --> pdb=" O TYR C 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 632 through 634 removed outlier: 11.292A pdb=" N LYS C 617 " --> pdb=" O ASN C 651 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ASN C 651 " --> pdb=" O LYS C 617 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ARG C 619 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 649 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 647 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER C 623 " --> pdb=" O GLY C 645 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY C 645 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 603 through 605 Processing sheet with id=AB6, first strand: chain 'C' and resid 673 through 675 Processing sheet with id=AB7, first strand: chain 'D' and resid 344 through 345 768 hydrogen bonds defined for protein. 2166 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: 3.26 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4654 1.33 - 1.45: 3708 1.45 - 1.57: 9680 1.57 - 1.70: 6 1.70 - 1.82: 146 Bond restraints: 18194 Sorted by residual: bond pdb=" C31 3PH B 603 " pdb=" O31 3PH B 603 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C31 3PH D 603 " pdb=" O31 3PH D 603 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C31 3PH B 602 " pdb=" O31 3PH B 602 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C31 3PH D 602 " pdb=" O31 3PH D 602 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C21 3PH B 602 " pdb=" O21 3PH B 602 " ideal model delta sigma weight residual 1.328 1.450 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 18189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 23520 1.99 - 3.99: 954 3.99 - 5.98: 170 5.98 - 7.98: 48 7.98 - 9.97: 30 Bond angle restraints: 24722 Sorted by residual: angle pdb=" N SER D 51 " pdb=" CA SER D 51 " pdb=" C SER D 51 " ideal model delta sigma weight residual 113.57 121.15 -7.58 1.38e+00 5.25e-01 3.01e+01 angle pdb=" N SER B 51 " pdb=" CA SER B 51 " pdb=" C SER B 51 " ideal model delta sigma weight residual 113.57 121.15 -7.58 1.38e+00 5.25e-01 3.01e+01 angle pdb=" C ASN B 209 " pdb=" N SER B 210 " pdb=" CA SER B 210 " ideal model delta sigma weight residual 120.63 129.39 -8.76 1.61e+00 3.86e-01 2.96e+01 angle pdb=" C ASN D 209 " pdb=" N SER D 210 " pdb=" CA SER D 210 " ideal model delta sigma weight residual 120.63 129.39 -8.76 1.61e+00 3.86e-01 2.96e+01 angle pdb=" C GLY C 260 " pdb=" N ASN C 261 " pdb=" CA ASN C 261 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.33e+01 ... (remaining 24717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.28: 10448 24.28 - 48.56: 460 48.56 - 72.84: 68 72.84 - 97.11: 28 97.11 - 121.39: 2 Dihedral angle restraints: 11006 sinusoidal: 4686 harmonic: 6320 Sorted by residual: dihedral pdb=" CB CYS C 114 " pdb=" SG CYS C 114 " pdb=" SG CYS D 144 " pdb=" CB CYS D 144 " ideal model delta sinusoidal sigma weight residual 93.00 146.82 -53.82 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CB CYS A 114 " pdb=" SG CYS A 114 " pdb=" SG CYS B 144 " pdb=" CB CYS B 144 " ideal model delta sinusoidal sigma weight residual 93.00 146.82 -53.82 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CA TYR A 259 " pdb=" C TYR A 259 " pdb=" N GLY A 260 " pdb=" CA GLY A 260 " ideal model delta harmonic sigma weight residual 180.00 152.37 27.63 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 11003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 2792 0.180 - 0.360: 16 0.360 - 0.540: 8 0.540 - 0.719: 2 0.719 - 0.899: 2 Chirality restraints: 2820 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 261 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.02e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 261 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.02e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 513 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.16e+00 ... (remaining 2817 not shown) Planarity restraints: 3070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 427 " 0.046 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO B 428 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 427 " -0.046 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO D 428 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 428 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 428 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 370 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C ASP B 370 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP B 370 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE B 371 " -0.015 2.00e-02 2.50e+03 ... (remaining 3067 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4660 2.79 - 3.32: 15481 3.32 - 3.85: 30686 3.85 - 4.37: 38358 4.37 - 4.90: 61174 Nonbonded interactions: 150359 Sorted by model distance: nonbonded pdb=" OG SER D 379 " pdb=" O HOH D 701 " model vdw 2.265 3.040 nonbonded pdb=" OG SER B 379 " pdb=" O HOH B 701 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP D 233 " pdb=" O HOH D 702 " model vdw 2.292 3.040 nonbonded pdb=" OD1 ASP B 233 " pdb=" O HOH B 702 " model vdw 2.292 3.040 nonbonded pdb=" O LEU D 238 " pdb=" OG1 THR D 242 " model vdw 2.302 3.040 ... (remaining 150354 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.270 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:9.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 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 0.122 18220 Z= 0.337 Angle : 1.058 14.773 24794 Z= 0.536 Chirality : 0.066 0.899 2820 Planarity : 0.007 0.069 3060 Dihedral : 14.647 121.392 6936 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.21 % Allowed : 3.59 % Favored : 96.20 % 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: -4.31 (0.14), residues: 2154 helix: -4.29 (0.07), residues: 1018 sheet: 0.35 (0.37), residues: 160 loop : -1.57 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 227 TYR 0.023 0.002 TYR C 65 PHE 0.028 0.002 PHE A 407 TRP 0.016 0.002 TRP C 443 HIS 0.007 0.002 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00753 (18194) covalent geometry : angle 1.00383 (24722) SS BOND : bond 0.00464 ( 6) SS BOND : angle 2.31682 ( 12) hydrogen bonds : bond 0.31415 ( 768) hydrogen bonds : angle 9.68061 ( 2166) link_BETA1-4 : bond 0.02296 ( 10) link_BETA1-4 : angle 6.85289 ( 30) link_NAG-ASN : bond 0.01577 ( 10) link_NAG-ASN : angle 6.75481 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 366 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.8749 (tmm) cc_final: 0.8544 (tmm) REVERT: A 381 MET cc_start: 0.8744 (ttp) cc_final: 0.8302 (ttp) REVERT: A 426 GLU cc_start: 0.7706 (pp20) cc_final: 0.7329 (pt0) REVERT: A 432 MET cc_start: 0.9053 (mmm) cc_final: 0.8573 (mmm) REVERT: A 465 MET cc_start: 0.9105 (mmm) cc_final: 0.8882 (mmm) REVERT: A 606 ASN cc_start: 0.8482 (t0) cc_final: 0.8184 (t0) REVERT: A 634 ASP cc_start: 0.7017 (p0) cc_final: 0.6750 (p0) REVERT: A 663 ARG cc_start: 0.7460 (tpt90) cc_final: 0.7211 (tpt90) REVERT: C 381 MET cc_start: 0.8756 (ttp) cc_final: 0.8303 (ttp) REVERT: C 426 GLU cc_start: 0.7705 (pp20) cc_final: 0.7326 (pt0) REVERT: C 432 MET cc_start: 0.9053 (mmm) cc_final: 0.8573 (mmm) REVERT: C 465 MET cc_start: 0.9107 (mmm) cc_final: 0.8881 (mmm) REVERT: C 606 ASN cc_start: 0.8481 (t0) cc_final: 0.8183 (t0) REVERT: C 634 ASP cc_start: 0.7016 (p0) cc_final: 0.6748 (p0) REVERT: C 663 ARG cc_start: 0.7463 (tpt90) cc_final: 0.7211 (tpt90) outliers start: 4 outliers final: 4 residues processed: 370 average time/residue: 0.6154 time to fit residues: 254.6622 Evaluate side-chains 252 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 248 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 668 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 135 ASN A 201 HIS A 220 HIS A 244 HIS A 324 HIS A 422 ASN A 442 ASN A 524 ASN A 598 ASN A 609 ASN A 654 ASN A 670 ASN B 271 ASN B 285 GLN B 336 HIS B 372 ASN C 125 GLN C 135 ASN C 201 HIS C 220 HIS C 244 HIS C 324 HIS C 422 ASN C 442 ASN C 524 ASN C 598 ASN C 609 ASN C 654 ASN C 670 ASN D 271 ASN D 285 GLN D 336 HIS D 372 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.210765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.148090 restraints weight = 15353.359| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.28 r_work: 0.3232 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18220 Z= 0.199 Angle : 0.838 12.598 24794 Z= 0.414 Chirality : 0.054 0.515 2820 Planarity : 0.007 0.066 3060 Dihedral : 11.526 110.490 2956 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 2.53 % Allowed : 9.50 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.10 (0.16), residues: 2154 helix: -1.75 (0.13), residues: 1024 sheet: 0.63 (0.37), residues: 162 loop : -1.18 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 405 TYR 0.020 0.002 TYR A 259 PHE 0.024 0.002 PHE C 407 TRP 0.016 0.002 TRP C 569 HIS 0.007 0.002 HIS D 472 Details of bonding type rmsd covalent geometry : bond 0.00422 (18194) covalent geometry : angle 0.80190 (24722) SS BOND : bond 0.02202 ( 6) SS BOND : angle 1.85907 ( 12) hydrogen bonds : bond 0.06872 ( 768) hydrogen bonds : angle 4.98541 ( 2166) link_BETA1-4 : bond 0.01535 ( 10) link_BETA1-4 : angle 4.38373 ( 30) link_NAG-ASN : bond 0.01323 ( 10) link_NAG-ASN : angle 5.51658 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.4873 (OUTLIER) cc_final: 0.4636 (mpt) REVERT: A 381 MET cc_start: 0.9341 (ttp) cc_final: 0.8959 (ttp) REVERT: A 546 ARG cc_start: 0.7739 (mpp80) cc_final: 0.7539 (mmm160) REVERT: A 634 ASP cc_start: 0.7314 (p0) cc_final: 0.6994 (p0) REVERT: A 663 ARG cc_start: 0.7692 (tpt90) cc_final: 0.7375 (tpt90) REVERT: B 53 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6601 (ttmm) REVERT: B 85 GLU cc_start: 0.4805 (OUTLIER) cc_final: 0.4103 (tt0) REVERT: B 166 ASN cc_start: 0.5926 (OUTLIER) cc_final: 0.5523 (m110) REVERT: B 308 PHE cc_start: 0.6934 (m-10) cc_final: 0.6507 (m-10) REVERT: B 326 ARG cc_start: 0.5682 (tpm170) cc_final: 0.5213 (tpp80) REVERT: C 68 MET cc_start: 0.4874 (OUTLIER) cc_final: 0.4633 (mpt) REVERT: C 381 MET cc_start: 0.9345 (ttp) cc_final: 0.8962 (ttp) REVERT: C 634 ASP cc_start: 0.7311 (p0) cc_final: 0.6990 (p0) REVERT: C 663 ARG cc_start: 0.7685 (tpt90) cc_final: 0.7368 (tpt90) REVERT: D 53 LYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6602 (ttmm) REVERT: D 85 GLU cc_start: 0.4801 (OUTLIER) cc_final: 0.4097 (tt0) REVERT: D 166 ASN cc_start: 0.5918 (OUTLIER) cc_final: 0.5512 (m110) REVERT: D 308 PHE cc_start: 0.6935 (m-10) cc_final: 0.6508 (m-10) REVERT: D 326 ARG cc_start: 0.5680 (tpm170) cc_final: 0.5215 (tpp80) outliers start: 48 outliers final: 11 residues processed: 316 average time/residue: 0.6349 time to fit residues: 224.1143 Evaluate side-chains 263 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 291 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 153 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 196 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 524 ASN A 609 ASN B 58 ASN C 501 ASN C 510 GLN C 524 ASN C 609 ASN D 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.210540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.133347 restraints weight = 15441.073| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.71 r_work: 0.3210 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18220 Z= 0.170 Angle : 0.785 11.746 24794 Z= 0.378 Chirality : 0.053 0.459 2820 Planarity : 0.005 0.055 3060 Dihedral : 10.011 59.209 2954 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.06 % Allowed : 10.93 % Favored : 86.01 % 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: -0.90 (0.17), residues: 2154 helix: -0.39 (0.15), residues: 1016 sheet: 0.82 (0.39), residues: 142 loop : -0.93 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 377 TYR 0.017 0.002 TYR A 259 PHE 0.024 0.002 PHE C 407 TRP 0.012 0.002 TRP D 230 HIS 0.005 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00353 (18194) covalent geometry : angle 0.73920 (24722) SS BOND : bond 0.01425 ( 6) SS BOND : angle 2.11726 ( 12) hydrogen bonds : bond 0.05960 ( 768) hydrogen bonds : angle 4.51085 ( 2166) link_BETA1-4 : bond 0.01540 ( 10) link_BETA1-4 : angle 5.08632 ( 30) link_NAG-ASN : bond 0.02304 ( 10) link_NAG-ASN : angle 5.58293 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 258 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.4186 (mpt) REVERT: A 381 MET cc_start: 0.9379 (ttp) cc_final: 0.9005 (ttp) REVERT: A 394 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8512 (m) REVERT: A 546 ARG cc_start: 0.7850 (mpp80) cc_final: 0.7424 (mtp-110) REVERT: A 634 ASP cc_start: 0.7232 (p0) cc_final: 0.6894 (p0) REVERT: A 653 LYS cc_start: 0.8145 (mttp) cc_final: 0.7885 (mptt) REVERT: A 663 ARG cc_start: 0.7715 (tpt90) cc_final: 0.7379 (tpt90) REVERT: B 53 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6551 (ttmm) REVERT: B 85 GLU cc_start: 0.4379 (OUTLIER) cc_final: 0.3758 (tt0) REVERT: B 166 ASN cc_start: 0.5923 (OUTLIER) cc_final: 0.5562 (m110) REVERT: B 205 LYS cc_start: 0.6046 (OUTLIER) cc_final: 0.5338 (ptpt) REVERT: B 216 LEU cc_start: 0.2417 (OUTLIER) cc_final: 0.2121 (pt) REVERT: B 308 PHE cc_start: 0.6738 (m-10) cc_final: 0.6361 (m-10) REVERT: B 346 VAL cc_start: 0.4830 (OUTLIER) cc_final: 0.4297 (m) REVERT: B 443 PHE cc_start: 0.4716 (OUTLIER) cc_final: 0.4482 (t80) REVERT: B 471 MET cc_start: 0.5093 (OUTLIER) cc_final: 0.4301 (mmt) REVERT: C 68 MET cc_start: 0.4878 (OUTLIER) cc_final: 0.4198 (mpt) REVERT: C 381 MET cc_start: 0.9382 (ttp) cc_final: 0.9004 (ttp) REVERT: C 394 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8523 (m) REVERT: C 634 ASP cc_start: 0.7230 (p0) cc_final: 0.6925 (p0) REVERT: C 653 LYS cc_start: 0.8142 (mttp) cc_final: 0.7881 (mptt) REVERT: C 663 ARG cc_start: 0.7716 (tpt90) cc_final: 0.7384 (tpt90) REVERT: D 53 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6549 (ttmm) REVERT: D 85 GLU cc_start: 0.4380 (OUTLIER) cc_final: 0.3764 (tt0) REVERT: D 166 ASN cc_start: 0.5922 (OUTLIER) cc_final: 0.5559 (m110) REVERT: D 205 LYS cc_start: 0.6036 (OUTLIER) cc_final: 0.5339 (ptpt) REVERT: D 216 LEU cc_start: 0.2408 (OUTLIER) cc_final: 0.2113 (pt) REVERT: D 308 PHE cc_start: 0.6749 (m-10) cc_final: 0.6372 (m-10) REVERT: D 346 VAL cc_start: 0.4837 (OUTLIER) cc_final: 0.4296 (m) REVERT: D 443 PHE cc_start: 0.4720 (OUTLIER) cc_final: 0.4487 (t80) REVERT: D 471 MET cc_start: 0.5087 (OUTLIER) cc_final: 0.4292 (mmt) outliers start: 58 outliers final: 16 residues processed: 302 average time/residue: 0.6102 time to fit residues: 206.1544 Evaluate side-chains 270 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 443 PHE Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 443 PHE Chi-restraints excluded: chain D residue 471 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 143 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 510 GLN A 524 ASN B 318 ASN C 501 ASN C 524 ASN D 318 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.210904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.130157 restraints weight = 15508.052| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.13 r_work: 0.3197 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18220 Z= 0.145 Angle : 0.720 10.559 24794 Z= 0.347 Chirality : 0.050 0.428 2820 Planarity : 0.005 0.048 3060 Dihedral : 9.522 59.075 2954 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.17 % Allowed : 10.77 % Favored : 86.06 % 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: -0.32 (0.18), residues: 2154 helix: 0.23 (0.16), residues: 1024 sheet: 0.79 (0.38), residues: 162 loop : -0.78 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 405 TYR 0.015 0.002 TYR D 240 PHE 0.021 0.002 PHE C 407 TRP 0.012 0.002 TRP A 431 HIS 0.004 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00304 (18194) covalent geometry : angle 0.68544 (24722) SS BOND : bond 0.00930 ( 6) SS BOND : angle 2.25048 ( 12) hydrogen bonds : bond 0.05197 ( 768) hydrogen bonds : angle 4.33530 ( 2166) link_BETA1-4 : bond 0.01225 ( 10) link_BETA1-4 : angle 3.99802 ( 30) link_NAG-ASN : bond 0.01192 ( 10) link_NAG-ASN : angle 4.87551 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 260 time to evaluate : 0.593 Fit side-chains REVERT: A 68 MET cc_start: 0.5243 (OUTLIER) cc_final: 0.4855 (mpm) REVERT: A 381 MET cc_start: 0.9383 (ttp) cc_final: 0.9011 (ttp) REVERT: A 394 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8494 (m) REVERT: A 546 ARG cc_start: 0.7746 (mpp80) cc_final: 0.7433 (mtp-110) REVERT: A 634 ASP cc_start: 0.7203 (p0) cc_final: 0.6913 (p0) REVERT: A 639 PHE cc_start: 0.7241 (t80) cc_final: 0.6909 (t80) REVERT: A 654 ASN cc_start: 0.7788 (m-40) cc_final: 0.7460 (m-40) REVERT: B 53 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6627 (ttmm) REVERT: B 85 GLU cc_start: 0.4581 (OUTLIER) cc_final: 0.3962 (tt0) REVERT: B 166 ASN cc_start: 0.5939 (OUTLIER) cc_final: 0.5598 (m110) REVERT: B 196 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5820 (mp) REVERT: B 205 LYS cc_start: 0.6197 (OUTLIER) cc_final: 0.5546 (ptpt) REVERT: B 216 LEU cc_start: 0.2381 (OUTLIER) cc_final: 0.2097 (pt) REVERT: B 270 MET cc_start: 0.6370 (mtp) cc_final: 0.5880 (tpp) REVERT: B 296 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6155 (mmm-85) REVERT: B 308 PHE cc_start: 0.6679 (m-10) cc_final: 0.6400 (m-10) REVERT: B 443 PHE cc_start: 0.4760 (OUTLIER) cc_final: 0.4558 (t80) REVERT: B 471 MET cc_start: 0.4904 (tpt) cc_final: 0.4055 (mmt) REVERT: B 484 GLU cc_start: 0.5004 (OUTLIER) cc_final: 0.4777 (tt0) REVERT: C 68 MET cc_start: 0.5227 (OUTLIER) cc_final: 0.4843 (mpm) REVERT: C 381 MET cc_start: 0.9383 (ttp) cc_final: 0.9008 (ttp) REVERT: C 394 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8496 (m) REVERT: C 634 ASP cc_start: 0.7203 (p0) cc_final: 0.6914 (p0) REVERT: C 639 PHE cc_start: 0.7254 (t80) cc_final: 0.6912 (t80) REVERT: C 654 ASN cc_start: 0.7785 (m-40) cc_final: 0.7454 (m-40) REVERT: D 53 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6620 (ttmm) REVERT: D 85 GLU cc_start: 0.4589 (OUTLIER) cc_final: 0.3971 (tt0) REVERT: D 166 ASN cc_start: 0.5941 (OUTLIER) cc_final: 0.5598 (m110) REVERT: D 196 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5812 (mp) REVERT: D 205 LYS cc_start: 0.6193 (OUTLIER) cc_final: 0.5541 (ptpt) REVERT: D 216 LEU cc_start: 0.2379 (OUTLIER) cc_final: 0.2093 (pt) REVERT: D 270 MET cc_start: 0.6365 (mtp) cc_final: 0.5877 (tpp) REVERT: D 296 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6147 (mmm-85) REVERT: D 308 PHE cc_start: 0.6681 (m-10) cc_final: 0.6401 (m-10) REVERT: D 443 PHE cc_start: 0.4768 (OUTLIER) cc_final: 0.4568 (t80) REVERT: D 471 MET cc_start: 0.4907 (tpt) cc_final: 0.4061 (mmt) REVERT: D 484 GLU cc_start: 0.5013 (OUTLIER) cc_final: 0.4786 (tt0) outliers start: 60 outliers final: 20 residues processed: 310 average time/residue: 0.6069 time to fit residues: 210.9050 Evaluate side-chains 274 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 443 PHE Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 296 ARG Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 PHE Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 143 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 460 GLN A 501 ASN A 524 ASN B 206 ASN C 244 HIS C 460 GLN C 501 ASN C 524 ASN D 206 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.208909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131513 restraints weight = 15376.252| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.86 r_work: 0.3191 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18220 Z= 0.183 Angle : 0.783 14.910 24794 Z= 0.379 Chirality : 0.053 0.478 2820 Planarity : 0.005 0.048 3060 Dihedral : 9.406 59.172 2954 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 3.91 % Allowed : 11.99 % Favored : 84.11 % 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: -0.18 (0.18), residues: 2154 helix: 0.40 (0.16), residues: 1012 sheet: 0.79 (0.38), residues: 162 loop : -0.74 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 405 TYR 0.017 0.002 TYR C 259 PHE 0.024 0.002 PHE A 407 TRP 0.011 0.002 TRP A 431 HIS 0.006 0.002 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00402 (18194) covalent geometry : angle 0.74891 (24722) SS BOND : bond 0.01244 ( 6) SS BOND : angle 2.55698 ( 12) hydrogen bonds : bond 0.05782 ( 768) hydrogen bonds : angle 4.48037 ( 2166) link_BETA1-4 : bond 0.01268 ( 10) link_BETA1-4 : angle 4.27705 ( 30) link_NAG-ASN : bond 0.01180 ( 10) link_NAG-ASN : angle 4.80589 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 255 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.4983 (mpt) REVERT: A 377 ARG cc_start: 0.8394 (mtp180) cc_final: 0.8104 (mmm160) REVERT: A 394 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8515 (m) REVERT: A 546 ARG cc_start: 0.7702 (mpp80) cc_final: 0.7473 (mtp-110) REVERT: A 634 ASP cc_start: 0.7345 (p0) cc_final: 0.7004 (p0) REVERT: A 654 ASN cc_start: 0.7851 (m-40) cc_final: 0.7530 (m-40) REVERT: B 53 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6629 (ttmm) REVERT: B 85 GLU cc_start: 0.4480 (OUTLIER) cc_final: 0.3975 (tt0) REVERT: B 166 ASN cc_start: 0.6010 (OUTLIER) cc_final: 0.5681 (m110) REVERT: B 196 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5898 (mp) REVERT: B 205 LYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5533 (ptpt) REVERT: B 216 LEU cc_start: 0.2657 (OUTLIER) cc_final: 0.2391 (pt) REVERT: B 308 PHE cc_start: 0.6716 (m-10) cc_final: 0.6388 (m-10) REVERT: B 326 ARG cc_start: 0.5478 (tpm170) cc_final: 0.4991 (tpp80) REVERT: B 443 PHE cc_start: 0.4798 (OUTLIER) cc_final: 0.4589 (t80) REVERT: B 484 GLU cc_start: 0.4801 (OUTLIER) cc_final: 0.4502 (tt0) REVERT: C 68 MET cc_start: 0.5356 (OUTLIER) cc_final: 0.4969 (mpt) REVERT: C 377 ARG cc_start: 0.8386 (mtp180) cc_final: 0.8096 (mmm160) REVERT: C 394 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8512 (m) REVERT: C 634 ASP cc_start: 0.7346 (p0) cc_final: 0.7037 (p0) REVERT: C 654 ASN cc_start: 0.7842 (m-40) cc_final: 0.7524 (m-40) REVERT: D 53 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6630 (ttmm) REVERT: D 85 GLU cc_start: 0.4486 (OUTLIER) cc_final: 0.3980 (tt0) REVERT: D 166 ASN cc_start: 0.6002 (OUTLIER) cc_final: 0.5673 (m110) REVERT: D 196 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5887 (mp) REVERT: D 205 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5538 (ptpt) REVERT: D 216 LEU cc_start: 0.2649 (OUTLIER) cc_final: 0.2382 (pt) REVERT: D 308 PHE cc_start: 0.6725 (m-10) cc_final: 0.6394 (m-10) REVERT: D 326 ARG cc_start: 0.5479 (tpm170) cc_final: 0.4993 (tpp80) REVERT: D 443 PHE cc_start: 0.4801 (OUTLIER) cc_final: 0.4595 (t80) REVERT: D 484 GLU cc_start: 0.4808 (OUTLIER) cc_final: 0.4511 (tt0) outliers start: 74 outliers final: 28 residues processed: 315 average time/residue: 0.5925 time to fit residues: 210.1144 Evaluate side-chains 269 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 443 PHE Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 443 PHE Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 182 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 211 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 460 GLN A 501 ASN C 244 HIS C 460 GLN C 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.209086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125526 restraints weight = 15256.195| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.80 r_work: 0.3164 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18220 Z= 0.179 Angle : 0.771 12.425 24794 Z= 0.375 Chirality : 0.053 0.452 2820 Planarity : 0.005 0.050 3060 Dihedral : 9.427 59.998 2954 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.75 % Allowed : 13.04 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2154 helix: 0.49 (0.16), residues: 1016 sheet: 0.82 (0.39), residues: 162 loop : -0.72 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 405 TYR 0.017 0.002 TYR A 259 PHE 0.024 0.002 PHE C 407 TRP 0.012 0.002 TRP A 431 HIS 0.006 0.002 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00393 (18194) covalent geometry : angle 0.73812 (24722) SS BOND : bond 0.01169 ( 6) SS BOND : angle 2.55336 ( 12) hydrogen bonds : bond 0.05612 ( 768) hydrogen bonds : angle 4.44728 ( 2166) link_BETA1-4 : bond 0.01317 ( 10) link_BETA1-4 : angle 4.31593 ( 30) link_NAG-ASN : bond 0.01049 ( 10) link_NAG-ASN : angle 4.61369 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 236 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.5487 (OUTLIER) cc_final: 0.5111 (mpm) REVERT: A 394 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8547 (m) REVERT: A 432 MET cc_start: 0.9325 (mmm) cc_final: 0.8967 (mmm) REVERT: A 546 ARG cc_start: 0.7866 (mpp80) cc_final: 0.7542 (mtp-110) REVERT: A 634 ASP cc_start: 0.7366 (p0) cc_final: 0.7015 (p0) REVERT: A 639 PHE cc_start: 0.7343 (t80) cc_final: 0.6942 (t80) REVERT: B 53 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6772 (ttmm) REVERT: B 85 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.4416 (tt0) REVERT: B 166 ASN cc_start: 0.6028 (OUTLIER) cc_final: 0.5699 (m-40) REVERT: B 196 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5642 (mp) REVERT: B 205 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5533 (ptpt) REVERT: B 216 LEU cc_start: 0.2406 (OUTLIER) cc_final: 0.2179 (pt) REVERT: B 270 MET cc_start: 0.6372 (mtp) cc_final: 0.6132 (tpp) REVERT: B 308 PHE cc_start: 0.6744 (m-10) cc_final: 0.6430 (m-10) REVERT: B 326 ARG cc_start: 0.5470 (tpm170) cc_final: 0.5012 (tpp80) REVERT: B 347 ARG cc_start: 0.4576 (OUTLIER) cc_final: 0.4302 (ttm170) REVERT: B 443 PHE cc_start: 0.4995 (OUTLIER) cc_final: 0.4745 (t80) REVERT: B 484 GLU cc_start: 0.4929 (OUTLIER) cc_final: 0.4610 (tt0) REVERT: C 68 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.5105 (mpm) REVERT: C 394 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8520 (m) REVERT: C 634 ASP cc_start: 0.7366 (p0) cc_final: 0.7013 (p0) REVERT: C 639 PHE cc_start: 0.7346 (t80) cc_final: 0.6943 (t80) REVERT: D 53 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6768 (ttmm) REVERT: D 85 GLU cc_start: 0.4915 (OUTLIER) cc_final: 0.4431 (tt0) REVERT: D 166 ASN cc_start: 0.6021 (OUTLIER) cc_final: 0.5692 (m-40) REVERT: D 196 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5627 (mp) REVERT: D 205 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5532 (ptpt) REVERT: D 216 LEU cc_start: 0.2397 (OUTLIER) cc_final: 0.2171 (pt) REVERT: D 270 MET cc_start: 0.6378 (mtp) cc_final: 0.6137 (tpp) REVERT: D 308 PHE cc_start: 0.6757 (m-10) cc_final: 0.6442 (m-10) REVERT: D 326 ARG cc_start: 0.5468 (tpm170) cc_final: 0.5010 (tpp80) REVERT: D 347 ARG cc_start: 0.4575 (OUTLIER) cc_final: 0.4299 (ttm170) REVERT: D 443 PHE cc_start: 0.4998 (OUTLIER) cc_final: 0.4752 (t80) REVERT: D 484 GLU cc_start: 0.4940 (OUTLIER) cc_final: 0.4622 (tt0) outliers start: 71 outliers final: 26 residues processed: 288 average time/residue: 0.6078 time to fit residues: 195.9804 Evaluate side-chains 267 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 443 PHE Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 443 PHE Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 44 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 73 optimal weight: 0.0370 chunk 132 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 GLN A 501 ASN C 330 GLN C 460 GLN C 501 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.210242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132679 restraints weight = 15458.544| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.60 r_work: 0.3183 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18220 Z= 0.123 Angle : 0.679 11.435 24794 Z= 0.325 Chirality : 0.048 0.385 2820 Planarity : 0.004 0.056 3060 Dihedral : 9.080 59.140 2954 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.85 % Allowed : 14.20 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.25 (0.18), residues: 2154 helix: 0.89 (0.16), residues: 1014 sheet: 0.85 (0.38), residues: 162 loop : -0.66 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 601 TYR 0.018 0.001 TYR D 104 PHE 0.016 0.001 PHE A 407 TRP 0.013 0.001 TRP C 431 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00250 (18194) covalent geometry : angle 0.64766 (24722) SS BOND : bond 0.00880 ( 6) SS BOND : angle 2.17344 ( 12) hydrogen bonds : bond 0.04485 ( 768) hydrogen bonds : angle 4.21805 ( 2166) link_BETA1-4 : bond 0.01194 ( 10) link_BETA1-4 : angle 3.96539 ( 30) link_NAG-ASN : bond 0.01097 ( 10) link_NAG-ASN : angle 4.18667 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 243 time to evaluate : 0.605 Fit side-chains REVERT: A 68 MET cc_start: 0.5305 (mpp) cc_final: 0.5028 (mpm) REVERT: A 377 ARG cc_start: 0.8346 (mtp180) cc_final: 0.7943 (mmm160) REVERT: A 494 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7196 (mp) REVERT: A 546 ARG cc_start: 0.7857 (mpp80) cc_final: 0.7572 (mtp-110) REVERT: A 634 ASP cc_start: 0.7135 (p0) cc_final: 0.6889 (p0) REVERT: A 639 PHE cc_start: 0.7265 (t80) cc_final: 0.6903 (t80) REVERT: A 663 ARG cc_start: 0.7706 (tpt90) cc_final: 0.7398 (tpt90) REVERT: B 53 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6644 (ttmm) REVERT: B 85 GLU cc_start: 0.4797 (OUTLIER) cc_final: 0.4481 (tt0) REVERT: B 166 ASN cc_start: 0.5996 (OUTLIER) cc_final: 0.5630 (m110) REVERT: B 196 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5620 (mp) REVERT: B 205 LYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5565 (mmtt) REVERT: B 337 MET cc_start: 0.6098 (tpp) cc_final: 0.5864 (tpt) REVERT: B 443 PHE cc_start: 0.4988 (OUTLIER) cc_final: 0.4709 (t80) REVERT: C 68 MET cc_start: 0.5292 (mpp) cc_final: 0.5018 (mpm) REVERT: C 377 ARG cc_start: 0.8348 (mtp180) cc_final: 0.8022 (mmm160) REVERT: C 494 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7197 (mp) REVERT: C 634 ASP cc_start: 0.7153 (p0) cc_final: 0.6911 (p0) REVERT: C 639 PHE cc_start: 0.7282 (t80) cc_final: 0.6910 (t80) REVERT: C 663 ARG cc_start: 0.7708 (tpt90) cc_final: 0.7401 (tpt90) REVERT: D 53 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6647 (ttmm) REVERT: D 85 GLU cc_start: 0.4810 (OUTLIER) cc_final: 0.4497 (tt0) REVERT: D 166 ASN cc_start: 0.5997 (OUTLIER) cc_final: 0.5630 (m110) REVERT: D 196 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5609 (mp) REVERT: D 205 LYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5614 (mmtt) REVERT: D 337 MET cc_start: 0.6196 (tpp) cc_final: 0.5971 (tpt) REVERT: D 443 PHE cc_start: 0.4990 (OUTLIER) cc_final: 0.4711 (t80) outliers start: 54 outliers final: 20 residues processed: 287 average time/residue: 0.6035 time to fit residues: 194.2242 Evaluate side-chains 251 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 443 PHE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 443 PHE Chi-restraints excluded: chain D residue 444 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 195 optimal weight: 0.6980 chunk 212 optimal weight: 0.0060 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 168 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 136 optimal weight: 0.2980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 501 ASN C 156 ASN C 501 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.211090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136062 restraints weight = 15472.621| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.88 r_work: 0.3210 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18220 Z= 0.114 Angle : 0.659 10.386 24794 Z= 0.314 Chirality : 0.048 0.375 2820 Planarity : 0.004 0.060 3060 Dihedral : 8.878 59.358 2954 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.22 % Allowed : 15.47 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2154 helix: 1.10 (0.16), residues: 1012 sheet: 0.87 (0.38), residues: 162 loop : -0.51 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 405 TYR 0.021 0.001 TYR D 104 PHE 0.013 0.001 PHE C 407 TRP 0.013 0.001 TRP A 431 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00227 (18194) covalent geometry : angle 0.63030 (24722) SS BOND : bond 0.00701 ( 6) SS BOND : angle 1.68995 ( 12) hydrogen bonds : bond 0.04129 ( 768) hydrogen bonds : angle 4.12516 ( 2166) link_BETA1-4 : bond 0.01100 ( 10) link_BETA1-4 : angle 3.70932 ( 30) link_NAG-ASN : bond 0.01071 ( 10) link_NAG-ASN : angle 4.09284 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.814 Fit side-chains REVERT: A 494 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7181 (mp) REVERT: A 539 ASP cc_start: 0.8865 (t70) cc_final: 0.8656 (t0) REVERT: A 546 ARG cc_start: 0.7853 (mpp80) cc_final: 0.7559 (mtp-110) REVERT: A 634 ASP cc_start: 0.7082 (p0) cc_final: 0.6851 (p0) REVERT: A 639 PHE cc_start: 0.7251 (t80) cc_final: 0.6888 (t80) REVERT: B 53 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6603 (ttmm) REVERT: B 85 GLU cc_start: 0.4691 (OUTLIER) cc_final: 0.4405 (tt0) REVERT: B 166 ASN cc_start: 0.6037 (OUTLIER) cc_final: 0.5665 (m-40) REVERT: B 196 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5428 (mp) REVERT: B 205 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5498 (mmtt) REVERT: B 337 MET cc_start: 0.6027 (tpp) cc_final: 0.5814 (tpt) REVERT: B 443 PHE cc_start: 0.5003 (OUTLIER) cc_final: 0.4696 (t80) REVERT: C 377 ARG cc_start: 0.8343 (mtp180) cc_final: 0.7946 (mmm160) REVERT: C 494 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7188 (mp) REVERT: C 539 ASP cc_start: 0.8860 (t70) cc_final: 0.8650 (t0) REVERT: C 634 ASP cc_start: 0.7086 (p0) cc_final: 0.6853 (p0) REVERT: C 639 PHE cc_start: 0.7250 (t80) cc_final: 0.6882 (t80) REVERT: D 53 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6605 (ttmm) REVERT: D 85 GLU cc_start: 0.4701 (OUTLIER) cc_final: 0.4412 (tt0) REVERT: D 166 ASN cc_start: 0.6039 (OUTLIER) cc_final: 0.5663 (m-40) REVERT: D 196 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5421 (mp) REVERT: D 205 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5489 (mmtt) REVERT: D 337 MET cc_start: 0.6057 (tpp) cc_final: 0.5833 (tpt) REVERT: D 443 PHE cc_start: 0.5004 (OUTLIER) cc_final: 0.4699 (t80) outliers start: 42 outliers final: 12 residues processed: 260 average time/residue: 0.6169 time to fit residues: 179.9507 Evaluate side-chains 229 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 443 PHE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 443 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 8 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 107 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN C 244 HIS C 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.208404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.165179 restraints weight = 15270.427| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 0.88 r_work: 0.3261 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18220 Z= 0.167 Angle : 0.746 10.407 24794 Z= 0.360 Chirality : 0.052 0.443 2820 Planarity : 0.005 0.062 3060 Dihedral : 8.985 59.899 2952 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.43 % Allowed : 15.31 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.37 (0.18), residues: 2154 helix: 0.95 (0.16), residues: 1012 sheet: 0.78 (0.38), residues: 162 loop : -0.54 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 452 TYR 0.018 0.002 TYR A 259 PHE 0.024 0.002 PHE A 407 TRP 0.009 0.002 TRP C 239 HIS 0.005 0.002 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00365 (18194) covalent geometry : angle 0.71687 (24722) SS BOND : bond 0.01150 ( 6) SS BOND : angle 2.24920 ( 12) hydrogen bonds : bond 0.05207 ( 768) hydrogen bonds : angle 4.33706 ( 2166) link_BETA1-4 : bond 0.01208 ( 10) link_BETA1-4 : angle 3.90645 ( 30) link_NAG-ASN : bond 0.01046 ( 10) link_NAG-ASN : angle 4.44054 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.690 Fit side-chains REVERT: A 494 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7321 (mp) REVERT: A 546 ARG cc_start: 0.8055 (mpp80) cc_final: 0.7808 (mtp-110) REVERT: A 634 ASP cc_start: 0.7386 (p0) cc_final: 0.7157 (p0) REVERT: B 53 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6882 (ttmm) REVERT: B 166 ASN cc_start: 0.6071 (OUTLIER) cc_final: 0.5724 (m-40) REVERT: B 196 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5628 (mp) REVERT: B 205 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.5791 (mmtt) REVERT: B 443 PHE cc_start: 0.4980 (OUTLIER) cc_final: 0.4698 (t80) REVERT: C 494 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7328 (mp) REVERT: C 634 ASP cc_start: 0.7390 (p0) cc_final: 0.7159 (p0) REVERT: D 53 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6895 (ttmm) REVERT: D 166 ASN cc_start: 0.6073 (OUTLIER) cc_final: 0.5725 (m-40) REVERT: D 196 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5610 (mp) REVERT: D 205 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.5795 (mmtt) REVERT: D 443 PHE cc_start: 0.4989 (OUTLIER) cc_final: 0.4703 (t80) outliers start: 46 outliers final: 18 residues processed: 259 average time/residue: 0.5799 time to fit residues: 169.6629 Evaluate side-chains 250 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 443 PHE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 443 PHE Chi-restraints excluded: chain D residue 444 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 140 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN C 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.209397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.167136 restraints weight = 15326.105| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 0.86 r_work: 0.3290 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18220 Z= 0.135 Angle : 0.716 10.236 24794 Z= 0.341 Chirality : 0.050 0.403 2820 Planarity : 0.004 0.062 3060 Dihedral : 8.900 59.527 2952 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.85 % Allowed : 16.05 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 2154 helix: 1.07 (0.16), residues: 1010 sheet: 0.81 (0.38), residues: 162 loop : -0.51 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 405 TYR 0.015 0.001 TYR C 259 PHE 0.021 0.001 PHE A 407 TRP 0.012 0.001 TRP C 569 HIS 0.004 0.001 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00285 (18194) covalent geometry : angle 0.68681 (24722) SS BOND : bond 0.00869 ( 6) SS BOND : angle 2.02566 ( 12) hydrogen bonds : bond 0.04700 ( 768) hydrogen bonds : angle 4.27992 ( 2166) link_BETA1-4 : bond 0.01156 ( 10) link_BETA1-4 : angle 3.89247 ( 30) link_NAG-ASN : bond 0.01028 ( 10) link_NAG-ASN : angle 4.20389 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 0.685 Fit side-chains REVERT: A 494 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7276 (mp) REVERT: A 546 ARG cc_start: 0.8096 (mpp80) cc_final: 0.7783 (mtp-110) REVERT: A 639 PHE cc_start: 0.7382 (t80) cc_final: 0.7178 (t80) REVERT: B 34 SER cc_start: 0.5151 (t) cc_final: 0.4947 (p) REVERT: B 53 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6851 (ttmm) REVERT: B 166 ASN cc_start: 0.6066 (OUTLIER) cc_final: 0.5716 (m110) REVERT: B 196 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.5509 (mp) REVERT: B 205 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.5794 (mmtt) REVERT: B 443 PHE cc_start: 0.4815 (OUTLIER) cc_final: 0.4525 (t80) REVERT: C 494 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7282 (mp) REVERT: C 639 PHE cc_start: 0.7377 (t80) cc_final: 0.7162 (t80) REVERT: D 34 SER cc_start: 0.5142 (t) cc_final: 0.4938 (p) REVERT: D 53 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6849 (ttmm) REVERT: D 166 ASN cc_start: 0.6065 (OUTLIER) cc_final: 0.5712 (m110) REVERT: D 196 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5519 (mp) REVERT: D 205 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.5792 (mmtt) REVERT: D 443 PHE cc_start: 0.4815 (OUTLIER) cc_final: 0.4523 (t80) outliers start: 35 outliers final: 18 residues processed: 254 average time/residue: 0.5967 time to fit residues: 170.3247 Evaluate side-chains 251 residues out of total 1894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 443 PHE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 443 PHE Chi-restraints excluded: chain D residue 444 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 43 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN B 166 ASN B 318 ASN C 501 ASN D 166 ASN D 318 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.206366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.163582 restraints weight = 15370.274| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 0.85 r_work: 0.3233 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18220 Z= 0.243 Angle : 0.872 11.209 24794 Z= 0.425 Chirality : 0.058 0.517 2820 Planarity : 0.006 0.061 3060 Dihedral : 9.441 59.052 2952 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 2.27 % Allowed : 16.31 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.18), residues: 2154 helix: 0.59 (0.16), residues: 1022 sheet: 0.80 (0.39), residues: 162 loop : -0.72 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 392 TYR 0.019 0.003 TYR C 259 PHE 0.027 0.003 PHE A 407 TRP 0.014 0.003 TRP C 443 HIS 0.009 0.002 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00547 (18194) covalent geometry : angle 0.83989 (24722) SS BOND : bond 0.01657 ( 6) SS BOND : angle 2.94757 ( 12) hydrogen bonds : bond 0.06229 ( 768) hydrogen bonds : angle 4.61364 ( 2166) link_BETA1-4 : bond 0.01434 ( 10) link_BETA1-4 : angle 4.42803 ( 30) link_NAG-ASN : bond 0.01047 ( 10) link_NAG-ASN : angle 4.85785 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9482.55 seconds wall clock time: 161 minutes 24.11 seconds (9684.11 seconds total)