Starting phenix.real_space_refine on Sun Aug 24 06:26:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wk6_37596/08_2025/8wk6_37596.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wk6_37596/08_2025/8wk6_37596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wk6_37596/08_2025/8wk6_37596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wk6_37596/08_2025/8wk6_37596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wk6_37596/08_2025/8wk6_37596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wk6_37596/08_2025/8wk6_37596.map" } resolution = 2.64 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= 0.004 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 84 5.16 5 C 11362 2.51 5 N 2824 2.21 5 O 3188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17460 Number of models: 1 Model: "" Number of chains: 16 Chain: "C" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5075 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 24, 'TRANS': 597} Chain: "B" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3514 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 23, 'TRANS': 426} Chain: "D" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5075 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 24, 'TRANS': 597} Chain: "A" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3514 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 23, 'TRANS': 426} 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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.92, per 1000 atoms: 0.22 Number of scatterers: 17460 At special positions: 0 Unit cell: (141.255, 84.315, 141.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 84 16.00 O 3188 8.00 N 2824 7.00 C 11362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 673 " - pdb=" SG CYS C 685 " distance=2.03 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 242 " - pdb=" SG CYS D 273 " distance=2.03 Simple disulfide: pdb=" SG CYS D 571 " - pdb=" SG CYS D 666 " distance=2.03 Simple disulfide: pdb=" SG CYS D 673 " - pdb=" SG CYS D 685 " 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 C 332 " " NAG F 1 " - " ASN C 575 " " NAG G 1 " - " ASN C 513 " " NAG H 1 " - " ASN C 261 " " NAG I 1 " - " ASN C 495 " " NAG J 1 " - " ASN D 332 " " NAG K 1 " - " ASN D 575 " " NAG L 1 " - " ASN D 513 " " NAG M 1 " - " ASN D 261 " " NAG N 1 " - " ASN D 495 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 724.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4044 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 16 sheets defined 57.7% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.668A pdb=" N PHE C 74 " --> pdb=" O LYS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 109 Proline residue: C 85 - end of helix Processing helix chain 'C' and resid 116 through 121 removed outlier: 3.510A pdb=" N GLU C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY C 121 " --> pdb=" O TRP C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 121' Processing helix chain 'C' and resid 127 through 131 removed outlier: 3.939A pdb=" N PHE C 131 " --> pdb=" O PRO C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 228 through 229 No H-bonds generated for 'chain 'C' and resid 228 through 229' Processing helix chain 'C' and resid 230 through 236 removed outlier: 3.533A pdb=" N TYR C 233 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 305 removed outlier: 3.647A pdb=" N GLN C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 340 removed outlier: 4.018A pdb=" N VAL C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 346 removed outlier: 4.015A pdb=" N LEU C 346 " --> pdb=" O TYR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 Processing helix chain 'C' and resid 370 through 373 removed outlier: 4.227A pdb=" N THR C 373 " --> pdb=" O GLN C 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 370 through 373' Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 395 through 398 Processing helix chain 'C' and resid 412 through 416 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 470 removed outlier: 3.607A pdb=" N ASN C 466 " --> pdb=" O VAL C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 547 through 561 removed outlier: 3.529A pdb=" N LEU C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 607 through 611 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 655 through 659 Processing helix chain 'B' and resid 17 through 28 removed outlier: 4.485A pdb=" N GLY B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 32 removed outlier: 3.588A pdb=" N PHE B 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 32' Processing helix chain 'B' and resid 33 through 41 removed outlier: 3.897A pdb=" N GLY B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 74 Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 89 through 121 removed outlier: 3.509A pdb=" N ALA B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 130 through 150 removed outlier: 3.720A pdb=" N LYS B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 185 removed outlier: 3.803A pdb=" N GLY B 185 " --> pdb=" O PHE B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 203 through 220 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 237 through 264 Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 289 through 319 Proline residue: B 313 - end of helix removed outlier: 4.011A pdb=" N GLN B 319 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 337 through 354 removed outlier: 3.520A pdb=" N THR B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 381 removed outlier: 3.726A pdb=" N LEU B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 396 through 417 removed outlier: 4.023A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 420 through 441 removed outlier: 3.550A pdb=" N LEU B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Proline residue: B 438 - end of helix Processing helix chain 'B' and resid 446 through 461 Processing helix chain 'D' and resid 69 through 74 removed outlier: 3.664A pdb=" N PHE D 74 " --> pdb=" O LYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 109 Proline residue: D 85 - end of helix Processing helix chain 'D' and resid 116 through 121 removed outlier: 3.506A pdb=" N GLU D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY D 121 " --> pdb=" O TRP D 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 121' Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.940A pdb=" N PHE D 131 " --> pdb=" O PRO D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 185 through 188 Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 228 through 229 No H-bonds generated for 'chain 'D' and resid 228 through 229' Processing helix chain 'D' and resid 230 through 236 removed outlier: 3.536A pdb=" N TYR D 233 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 235 " --> pdb=" O LYS D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 305 removed outlier: 3.648A pdb=" N GLN D 293 " --> pdb=" O ASN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 340 removed outlier: 4.021A pdb=" N VAL D 340 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 346 removed outlier: 4.009A pdb=" N LEU D 346 " --> pdb=" O TYR D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 369 Processing helix chain 'D' and resid 370 through 373 removed outlier: 4.225A pdb=" N THR D 373 " --> pdb=" O GLN D 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 373' Processing helix chain 'D' and resid 389 through 394 Processing helix chain 'D' and resid 395 through 398 Processing helix chain 'D' and resid 412 through 416 Processing helix chain 'D' and resid 420 through 435 Processing helix chain 'D' and resid 452 through 457 Processing helix chain 'D' and resid 458 through 460 No H-bonds generated for 'chain 'D' and resid 458 through 460' Processing helix chain 'D' and resid 461 through 470 removed outlier: 3.608A pdb=" N ASN D 466 " --> pdb=" O VAL D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 547 through 561 removed outlier: 3.530A pdb=" N LEU D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 Processing helix chain 'D' and resid 607 through 611 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 655 through 659 Processing helix chain 'A' and resid 17 through 28 removed outlier: 4.495A pdb=" N GLY A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 32 removed outlier: 3.591A pdb=" N PHE A 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 29 through 32' Processing helix chain 'A' and resid 33 through 41 removed outlier: 3.906A pdb=" N GLY A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 74 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 89 through 121 removed outlier: 3.548A pdb=" N ALA A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 130 through 150 removed outlier: 3.719A pdb=" N LYS A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 185 removed outlier: 3.807A pdb=" N GLY A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 203 through 220 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 237 through 264 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 265 through 272 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 289 through 319 Proline residue: A 313 - end of helix removed outlier: 4.001A pdb=" N GLN A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 337 through 354 removed outlier: 3.522A pdb=" N THR A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 381 removed outlier: 3.671A pdb=" N LEU A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 396 through 417 removed outlier: 4.024A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 420 through 441 removed outlier: 3.552A pdb=" N LEU A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Proline residue: A 438 - end of helix Processing helix chain 'A' and resid 446 through 461 Processing sheet with id=AA1, first strand: chain 'C' and resid 380 through 384 removed outlier: 7.044A pdb=" N LEU C 207 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N SER C 312 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 209 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP C 314 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE C 211 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR C 124 " --> pdb=" O TRP C 161 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N MET C 123 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP C 443 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N TYR C 479 " --> pdb=" O TRP C 443 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 166 through 170 removed outlier: 7.130A pdb=" N LYS C 167 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY C 176 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AA4, first strand: chain 'C' and resid 243 through 245 removed outlier: 3.928A pdb=" N THR C 243 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 632 through 634 removed outlier: 11.126A pdb=" N MET C 618 " --> pdb=" O ASN C 651 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N ASN C 651 " --> pdb=" O MET C 618 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 620 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU C 649 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C 644 " --> pdb=" O ASN C 598 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 585 " --> pdb=" O TRP C 569 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 603 through 606 Processing sheet with id=AA7, first strand: chain 'C' and resid 673 through 675 Processing sheet with id=AA8, first strand: chain 'B' and resid 330 through 331 Processing sheet with id=AA9, first strand: chain 'D' and resid 380 through 384 removed outlier: 7.044A pdb=" N LEU D 207 " --> pdb=" O GLY D 310 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N SER D 312 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE D 209 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP D 314 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE D 211 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR D 124 " --> pdb=" O TRP D 161 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET D 123 " --> pdb=" O THR D 478 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP D 443 " --> pdb=" O ILE D 477 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N TYR D 479 " --> pdb=" O TRP D 443 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 166 through 170 removed outlier: 7.132A pdb=" N LYS D 167 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY D 176 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 239 through 240 Processing sheet with id=AB3, first strand: chain 'D' and resid 243 through 245 removed outlier: 3.929A pdb=" N THR D 243 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 632 through 634 removed outlier: 11.128A pdb=" N MET D 618 " --> pdb=" O ASN D 651 " (cutoff:3.500A) removed outlier: 11.023A pdb=" N ASN D 651 " --> pdb=" O MET D 618 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE D 620 " --> pdb=" O GLU D 649 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLU D 649 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 644 " --> pdb=" O ASN D 598 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 585 " --> pdb=" O TRP D 569 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 603 through 606 Processing sheet with id=AB6, first strand: chain 'D' and resid 673 through 675 Processing sheet with id=AB7, first strand: chain 'A' and resid 330 through 331 864 hydrogen bonds defined for protein. 2436 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: 2.60 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5285 1.34 - 1.46: 3204 1.46 - 1.58: 9295 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 17916 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 17911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 23746 1.47 - 2.93: 507 2.93 - 4.40: 86 4.40 - 5.86: 32 5.86 - 7.33: 9 Bond angle restraints: 24380 Sorted by residual: angle pdb=" N VAL B 190 " pdb=" CA VAL B 190 " pdb=" C VAL B 190 " ideal model delta sigma weight residual 113.53 109.81 3.72 9.80e-01 1.04e+00 1.44e+01 angle pdb=" N VAL A 190 " pdb=" CA VAL A 190 " pdb=" C VAL A 190 " ideal model delta sigma weight residual 113.53 109.81 3.72 9.80e-01 1.04e+00 1.44e+01 angle pdb=" N ILE A 412 " pdb=" CA ILE A 412 " pdb=" C ILE A 412 " ideal model delta sigma weight residual 108.88 115.18 -6.30 2.16e+00 2.14e-01 8.50e+00 angle pdb=" N ILE B 412 " pdb=" CA ILE B 412 " pdb=" C ILE B 412 " ideal model delta sigma weight residual 108.88 115.13 -6.25 2.16e+00 2.14e-01 8.38e+00 angle pdb=" C ILE B 437 " pdb=" CA ILE B 437 " pdb=" CB ILE B 437 " ideal model delta sigma weight residual 114.00 110.36 3.64 1.31e+00 5.83e-01 7.72e+00 ... (remaining 24375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 10192 24.81 - 49.63: 436 49.63 - 74.44: 77 74.44 - 99.25: 39 99.25 - 124.07: 50 Dihedral angle restraints: 10794 sinusoidal: 4514 harmonic: 6280 Sorted by residual: dihedral pdb=" CB CYS D 673 " pdb=" SG CYS D 673 " pdb=" SG CYS D 685 " pdb=" CB CYS D 685 " ideal model delta sinusoidal sigma weight residual 93.00 129.09 -36.09 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CB CYS C 673 " pdb=" SG CYS C 673 " pdb=" SG CYS C 685 " pdb=" CB CYS C 685 " ideal model delta sinusoidal sigma weight residual 93.00 129.00 -36.00 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " pdb=" C5 NAG I 2 " ideal model delta sinusoidal sigma weight residual -62.96 61.11 -124.07 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 10791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2114 0.045 - 0.090: 552 0.090 - 0.135: 131 0.135 - 0.180: 16 0.180 - 0.226: 5 Chirality restraints: 2818 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 6.52e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.44e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN D 575 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2815 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.322 2.00e-02 2.50e+03 2.70e-01 9.14e+02 pdb=" C7 NAG E 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.194 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.465 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.289 2.00e-02 2.50e+03 2.42e-01 7.34e+02 pdb=" C7 NAG E 1 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.411 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " -0.285 2.00e-02 2.50e+03 2.38e-01 7.08e+02 pdb=" C7 NAG J 1 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " 0.403 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.007 2.00e-02 2.50e+03 ... (remaining 3019 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1203 2.74 - 3.28: 18316 3.28 - 3.82: 29126 3.82 - 4.36: 34254 4.36 - 4.90: 57940 Nonbonded interactions: 140839 Sorted by model distance: nonbonded pdb=" O PHE B 32 " pdb=" OH TYR B 118 " model vdw 2.198 3.040 nonbonded pdb=" O PHE A 32 " pdb=" OH TYR A 118 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR C 471 " pdb=" OH TYR C 582 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR D 471 " pdb=" OH TYR D 582 " model vdw 2.223 3.040 nonbonded pdb=" O ILE A 258 " pdb=" OG1 THR A 262 " model vdw 2.223 3.040 ... (remaining 140834 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 'B' } ncs_group { reference = chain 'C' 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: 1.050 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.280 Find NCS groups from input model: 0.290 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.003 0.083 17944 Z= 0.153 Angle : 0.573 7.331 24456 Z= 0.293 Chirality : 0.043 0.226 2818 Planarity : 0.009 0.270 3012 Dihedral : 17.808 124.068 6726 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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 aren not related in a simple way. whole: 0.65 (0.19), residues: 2136 helix: 1.63 (0.17), residues: 1018 sheet: -0.19 (0.37), residues: 196 loop : -0.78 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 663 TYR 0.019 0.001 TYR C 236 PHE 0.022 0.001 PHE A 364 TRP 0.065 0.002 TRP B 53 HIS 0.002 0.000 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00302 (17916) covalent geometry : angle 0.56101 (24380) SS BOND : bond 0.00166 ( 8) SS BOND : angle 0.38169 ( 16) hydrogen bonds : bond 0.15957 ( 864) hydrogen bonds : angle 5.37642 ( 2436) link_BETA1-4 : bond 0.00851 ( 10) link_BETA1-4 : angle 2.62020 ( 30) link_NAG-ASN : bond 0.00460 ( 10) link_NAG-ASN : angle 2.31619 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 452 MET cc_start: 0.8719 (mmp) cc_final: 0.8362 (mmm) REVERT: D 509 MET cc_start: 0.9482 (tpt) cc_final: 0.9258 (tpt) REVERT: A 44 MET cc_start: 0.8831 (mpp) cc_final: 0.8554 (mmm) REVERT: A 452 MET cc_start: 0.8727 (mmp) cc_final: 0.8366 (mmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.5234 time to fit residues: 67.2823 Evaluate side-chains 91 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 40.0000 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 625 ASN ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN A 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.095755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.054227 restraints weight = 45850.103| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.14 r_work: 0.2550 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17944 Z= 0.168 Angle : 0.639 12.868 24456 Z= 0.308 Chirality : 0.046 0.291 2818 Planarity : 0.004 0.051 3012 Dihedral : 16.287 112.220 2742 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.31 % Allowed : 5.66 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.19), residues: 2136 helix: 1.69 (0.17), residues: 1050 sheet: 0.32 (0.44), residues: 146 loop : -0.65 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 546 TYR 0.023 0.001 TYR C 236 PHE 0.022 0.001 PHE A 364 TRP 0.047 0.002 TRP B 53 HIS 0.002 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00380 (17916) covalent geometry : angle 0.62414 (24380) SS BOND : bond 0.00220 ( 8) SS BOND : angle 0.44548 ( 16) hydrogen bonds : bond 0.04813 ( 864) hydrogen bonds : angle 4.48626 ( 2436) link_BETA1-4 : bond 0.01126 ( 10) link_BETA1-4 : angle 3.29752 ( 30) link_NAG-ASN : bond 0.00481 ( 10) link_NAG-ASN : angle 2.28238 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 452 MET cc_start: 0.8714 (mmp) cc_final: 0.8361 (mmm) REVERT: A 452 MET cc_start: 0.8717 (mmp) cc_final: 0.8360 (mmm) outliers start: 6 outliers final: 4 residues processed: 96 average time/residue: 0.5156 time to fit residues: 55.7996 Evaluate side-chains 92 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 210 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 170 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.095001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.053291 restraints weight = 46092.585| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 3.16 r_work: 0.2527 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17944 Z= 0.192 Angle : 0.629 12.468 24456 Z= 0.302 Chirality : 0.044 0.235 2818 Planarity : 0.004 0.058 3012 Dihedral : 14.736 112.700 2742 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.52 % Allowed : 7.60 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.18), residues: 2136 helix: 1.87 (0.17), residues: 1038 sheet: 0.41 (0.44), residues: 146 loop : -0.70 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 546 TYR 0.018 0.001 TYR C 236 PHE 0.024 0.001 PHE B 364 TRP 0.044 0.002 TRP B 53 HIS 0.002 0.001 HIS C 244 Details of bonding type rmsd covalent geometry : bond 0.00437 (17916) covalent geometry : angle 0.61443 (24380) SS BOND : bond 0.00248 ( 8) SS BOND : angle 0.45072 ( 16) hydrogen bonds : bond 0.04778 ( 864) hydrogen bonds : angle 4.36779 ( 2436) link_BETA1-4 : bond 0.01049 ( 10) link_BETA1-4 : angle 3.03639 ( 30) link_NAG-ASN : bond 0.00321 ( 10) link_NAG-ASN : angle 2.51346 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: C 663 ARG cc_start: 0.8903 (mtm-85) cc_final: 0.8536 (mtm-85) REVERT: B 44 MET cc_start: 0.8586 (mpt) cc_final: 0.8357 (mmm) REVERT: B 53 TRP cc_start: 0.6305 (m-10) cc_final: 0.6082 (m-10) REVERT: B 452 MET cc_start: 0.8708 (mmp) cc_final: 0.8372 (mmm) REVERT: D 663 ARG cc_start: 0.8898 (mtm-85) cc_final: 0.8528 (mtm-85) REVERT: A 452 MET cc_start: 0.8729 (mmp) cc_final: 0.8374 (mmm) outliers start: 10 outliers final: 0 residues processed: 92 average time/residue: 0.6470 time to fit residues: 66.7318 Evaluate side-chains 85 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 143 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 0.0970 chunk 81 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.094841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.053161 restraints weight = 46075.067| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.17 r_work: 0.2522 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17944 Z= 0.183 Angle : 0.619 11.720 24456 Z= 0.297 Chirality : 0.044 0.244 2818 Planarity : 0.004 0.057 3012 Dihedral : 13.480 112.009 2742 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.10 % Allowed : 8.33 % Favored : 90.57 % 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 aren not related in a simple way. whole: 1.02 (0.18), residues: 2136 helix: 1.92 (0.17), residues: 1038 sheet: 0.42 (0.44), residues: 146 loop : -0.70 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 546 TYR 0.017 0.001 TYR C 236 PHE 0.024 0.001 PHE A 364 TRP 0.034 0.002 TRP B 98 HIS 0.002 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00419 (17916) covalent geometry : angle 0.60323 (24380) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.45290 ( 16) hydrogen bonds : bond 0.04568 ( 864) hydrogen bonds : angle 4.26068 ( 2436) link_BETA1-4 : bond 0.01190 ( 10) link_BETA1-4 : angle 3.21886 ( 30) link_NAG-ASN : bond 0.00304 ( 10) link_NAG-ASN : angle 2.48720 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 TRP cc_start: 0.6567 (m-10) cc_final: 0.6269 (m-10) REVERT: B 69 GLU cc_start: 0.9130 (tt0) cc_final: 0.8845 (tm-30) REVERT: B 452 MET cc_start: 0.8675 (mmp) cc_final: 0.8319 (mmm) REVERT: A 44 MET cc_start: 0.8625 (mpt) cc_final: 0.8388 (mmm) REVERT: A 452 MET cc_start: 0.8700 (mmp) cc_final: 0.8353 (mmm) outliers start: 21 outliers final: 2 residues processed: 107 average time/residue: 0.6408 time to fit residues: 77.0817 Evaluate side-chains 86 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.094468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052673 restraints weight = 45983.076| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 3.15 r_work: 0.2508 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17944 Z= 0.201 Angle : 0.634 11.979 24456 Z= 0.305 Chirality : 0.044 0.238 2818 Planarity : 0.004 0.055 3012 Dihedral : 12.860 111.314 2742 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.79 % Allowed : 9.22 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.18), residues: 2136 helix: 1.96 (0.16), residues: 1038 sheet: 0.45 (0.41), residues: 166 loop : -0.78 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 546 TYR 0.017 0.001 TYR A 118 PHE 0.025 0.001 PHE B 364 TRP 0.035 0.002 TRP B 98 HIS 0.003 0.001 HIS D 348 Details of bonding type rmsd covalent geometry : bond 0.00463 (17916) covalent geometry : angle 0.61892 (24380) SS BOND : bond 0.00278 ( 8) SS BOND : angle 0.51900 ( 16) hydrogen bonds : bond 0.04664 ( 864) hydrogen bonds : angle 4.23489 ( 2436) link_BETA1-4 : bond 0.01126 ( 10) link_BETA1-4 : angle 3.42359 ( 30) link_NAG-ASN : bond 0.00245 ( 10) link_NAG-ASN : angle 2.20958 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: B 53 TRP cc_start: 0.6736 (m-10) cc_final: 0.6392 (m-10) REVERT: B 452 MET cc_start: 0.8537 (mmp) cc_final: 0.8211 (mmm) REVERT: D 509 MET cc_start: 0.9544 (OUTLIER) cc_final: 0.8523 (tpt) REVERT: A 44 MET cc_start: 0.8592 (mpt) cc_final: 0.8387 (mmm) REVERT: A 452 MET cc_start: 0.8567 (mmp) cc_final: 0.8247 (mmm) outliers start: 15 outliers final: 4 residues processed: 96 average time/residue: 0.5589 time to fit residues: 61.0663 Evaluate side-chains 89 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain A residue 157 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 8 optimal weight: 0.0270 chunk 185 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.3040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.095743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.054119 restraints weight = 45792.816| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.16 r_work: 0.2547 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17944 Z= 0.119 Angle : 0.607 11.316 24456 Z= 0.287 Chirality : 0.043 0.275 2818 Planarity : 0.004 0.051 3012 Dihedral : 12.079 110.361 2742 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.63 % Allowed : 9.64 % Favored : 89.73 % 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 aren not related in a simple way. whole: 1.06 (0.18), residues: 2136 helix: 1.96 (0.16), residues: 1040 sheet: 0.42 (0.44), residues: 146 loop : -0.68 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 663 TYR 0.010 0.001 TYR A 218 PHE 0.024 0.001 PHE B 364 TRP 0.034 0.001 TRP A 98 HIS 0.002 0.000 HIS D 657 Details of bonding type rmsd covalent geometry : bond 0.00259 (17916) covalent geometry : angle 0.58949 (24380) SS BOND : bond 0.00169 ( 8) SS BOND : angle 0.34234 ( 16) hydrogen bonds : bond 0.04054 ( 864) hydrogen bonds : angle 4.08729 ( 2436) link_BETA1-4 : bond 0.01147 ( 10) link_BETA1-4 : angle 3.71833 ( 30) link_NAG-ASN : bond 0.00386 ( 10) link_NAG-ASN : angle 2.13646 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: C 68 MET cc_start: 0.6785 (mmm) cc_final: 0.6542 (mmm) REVERT: C 113 LYS cc_start: 0.9321 (ttpp) cc_final: 0.9056 (tppt) REVERT: C 509 MET cc_start: 0.9588 (tpt) cc_final: 0.9282 (tpt) REVERT: C 663 ARG cc_start: 0.8890 (mtm-85) cc_final: 0.8575 (mtm-85) REVERT: B 53 TRP cc_start: 0.6760 (m-10) cc_final: 0.6347 (m-10) REVERT: B 452 MET cc_start: 0.8523 (mmp) cc_final: 0.8189 (mmm) REVERT: D 68 MET cc_start: 0.6886 (mmm) cc_final: 0.6640 (mmm) REVERT: D 113 LYS cc_start: 0.9323 (ttpp) cc_final: 0.9057 (tppt) REVERT: D 663 ARG cc_start: 0.8891 (mtm-85) cc_final: 0.8573 (mtm-85) REVERT: A 44 MET cc_start: 0.8601 (mpt) cc_final: 0.8392 (mmm) REVERT: A 452 MET cc_start: 0.8554 (mmp) cc_final: 0.8219 (mmm) outliers start: 12 outliers final: 6 residues processed: 93 average time/residue: 0.5723 time to fit residues: 59.9031 Evaluate side-chains 90 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain A residue 157 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 119 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 ASN D 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.094931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.053193 restraints weight = 45976.189| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.17 r_work: 0.2521 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17944 Z= 0.162 Angle : 0.611 11.444 24456 Z= 0.290 Chirality : 0.044 0.304 2818 Planarity : 0.004 0.048 3012 Dihedral : 11.347 109.002 2742 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.63 % Allowed : 9.96 % Favored : 89.41 % 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 aren not related in a simple way. whole: 1.18 (0.18), residues: 2136 helix: 2.11 (0.16), residues: 1028 sheet: 0.56 (0.41), residues: 164 loop : -0.68 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 663 TYR 0.012 0.001 TYR A 118 PHE 0.025 0.001 PHE A 364 TRP 0.036 0.001 TRP B 98 HIS 0.002 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00371 (17916) covalent geometry : angle 0.59245 (24380) SS BOND : bond 0.00245 ( 8) SS BOND : angle 0.44474 ( 16) hydrogen bonds : bond 0.04305 ( 864) hydrogen bonds : angle 4.10266 ( 2436) link_BETA1-4 : bond 0.01139 ( 10) link_BETA1-4 : angle 3.79747 ( 30) link_NAG-ASN : bond 0.00263 ( 10) link_NAG-ASN : angle 2.17869 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 MET cc_start: 0.6672 (mmm) cc_final: 0.6456 (mmm) REVERT: B 53 TRP cc_start: 0.6804 (m-10) cc_final: 0.6405 (m-10) REVERT: B 452 MET cc_start: 0.8541 (mmp) cc_final: 0.8213 (mmm) REVERT: D 68 MET cc_start: 0.6743 (mmm) cc_final: 0.6522 (mmm) REVERT: A 44 MET cc_start: 0.8588 (mpt) cc_final: 0.8357 (mmm) REVERT: A 452 MET cc_start: 0.8562 (mmp) cc_final: 0.8234 (mmm) outliers start: 12 outliers final: 6 residues processed: 95 average time/residue: 0.5199 time to fit residues: 55.8641 Evaluate side-chains 90 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain A residue 157 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 142 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.093887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.051909 restraints weight = 46005.150| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.18 r_work: 0.2499 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17944 Z= 0.210 Angle : 0.655 13.219 24456 Z= 0.311 Chirality : 0.045 0.316 2818 Planarity : 0.004 0.043 3012 Dihedral : 10.581 107.889 2742 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.63 % Allowed : 10.17 % Favored : 89.20 % 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 aren not related in a simple way. whole: 1.17 (0.18), residues: 2136 helix: 2.07 (0.16), residues: 1032 sheet: 0.60 (0.41), residues: 164 loop : -0.67 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 663 TYR 0.018 0.001 TYR A 118 PHE 0.028 0.001 PHE A 364 TRP 0.043 0.002 TRP B 98 HIS 0.006 0.001 HIS C 244 Details of bonding type rmsd covalent geometry : bond 0.00483 (17916) covalent geometry : angle 0.63773 (24380) SS BOND : bond 0.00271 ( 8) SS BOND : angle 0.51138 ( 16) hydrogen bonds : bond 0.04670 ( 864) hydrogen bonds : angle 4.16861 ( 2436) link_BETA1-4 : bond 0.01165 ( 10) link_BETA1-4 : angle 3.77283 ( 30) link_NAG-ASN : bond 0.00186 ( 10) link_NAG-ASN : angle 2.27774 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 LYS cc_start: 0.9378 (ttpp) cc_final: 0.9097 (tppt) REVERT: B 53 TRP cc_start: 0.6897 (m100) cc_final: 0.6553 (m-10) REVERT: B 452 MET cc_start: 0.8586 (mmp) cc_final: 0.8241 (mmm) REVERT: D 68 MET cc_start: 0.6802 (mmm) cc_final: 0.6572 (mmm) REVERT: D 113 LYS cc_start: 0.9373 (ttpp) cc_final: 0.9093 (tppt) REVERT: A 452 MET cc_start: 0.8611 (mmp) cc_final: 0.8255 (mmm) outliers start: 12 outliers final: 8 residues processed: 91 average time/residue: 0.5862 time to fit residues: 60.4967 Evaluate side-chains 92 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain A residue 157 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 92 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 210 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.095017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.053218 restraints weight = 45885.798| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 3.17 r_work: 0.2522 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17944 Z= 0.153 Angle : 0.623 12.432 24456 Z= 0.294 Chirality : 0.044 0.319 2818 Planarity : 0.003 0.042 3012 Dihedral : 9.840 106.822 2742 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.42 % Allowed : 10.43 % Favored : 89.15 % 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 aren not related in a simple way. whole: 1.27 (0.18), residues: 2136 helix: 2.18 (0.16), residues: 1020 sheet: 0.87 (0.42), residues: 160 loop : -0.67 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 663 TYR 0.011 0.001 TYR A 118 PHE 0.027 0.001 PHE A 364 TRP 0.043 0.002 TRP B 98 HIS 0.002 0.001 HIS D 348 Details of bonding type rmsd covalent geometry : bond 0.00346 (17916) covalent geometry : angle 0.60382 (24380) SS BOND : bond 0.00240 ( 8) SS BOND : angle 0.44574 ( 16) hydrogen bonds : bond 0.04251 ( 864) hydrogen bonds : angle 4.07275 ( 2436) link_BETA1-4 : bond 0.01192 ( 10) link_BETA1-4 : angle 3.89223 ( 30) link_NAG-ASN : bond 0.00268 ( 10) link_NAG-ASN : angle 2.20141 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: C 113 LYS cc_start: 0.9369 (ttpp) cc_final: 0.9098 (tppt) REVERT: C 509 MET cc_start: 0.9582 (tpt) cc_final: 0.9307 (tpt) REVERT: C 663 ARG cc_start: 0.8886 (mtm-85) cc_final: 0.8430 (mtm-85) REVERT: B 53 TRP cc_start: 0.6870 (m100) cc_final: 0.6515 (m-10) REVERT: B 452 MET cc_start: 0.8580 (mmp) cc_final: 0.8234 (mmm) REVERT: D 68 MET cc_start: 0.6513 (mmm) cc_final: 0.6306 (mmm) REVERT: D 663 ARG cc_start: 0.8885 (mtm-85) cc_final: 0.8425 (mtm-85) REVERT: A 452 MET cc_start: 0.8604 (mmp) cc_final: 0.8251 (mmm) outliers start: 8 outliers final: 8 residues processed: 90 average time/residue: 0.5165 time to fit residues: 52.6135 Evaluate side-chains 92 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain A residue 157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 212 optimal weight: 20.0000 chunk 175 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 202 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.095059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.053254 restraints weight = 45594.979| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.17 r_work: 0.2524 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17944 Z= 0.151 Angle : 0.632 12.864 24456 Z= 0.297 Chirality : 0.044 0.330 2818 Planarity : 0.003 0.042 3012 Dihedral : 9.298 105.486 2742 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.31 % Allowed : 10.53 % Favored : 89.15 % 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 aren not related in a simple way. whole: 1.29 (0.18), residues: 2136 helix: 2.19 (0.16), residues: 1018 sheet: 0.89 (0.42), residues: 160 loop : -0.63 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 663 TYR 0.012 0.001 TYR A 118 PHE 0.026 0.001 PHE B 364 TRP 0.045 0.002 TRP B 98 HIS 0.002 0.001 HIS D 348 Details of bonding type rmsd covalent geometry : bond 0.00341 (17916) covalent geometry : angle 0.61292 (24380) SS BOND : bond 0.00207 ( 8) SS BOND : angle 0.40442 ( 16) hydrogen bonds : bond 0.04208 ( 864) hydrogen bonds : angle 4.05392 ( 2436) link_BETA1-4 : bond 0.01178 ( 10) link_BETA1-4 : angle 3.93206 ( 30) link_NAG-ASN : bond 0.00256 ( 10) link_NAG-ASN : angle 2.20829 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: C 68 MET cc_start: 0.6222 (mmm) cc_final: 0.5885 (mpt) REVERT: C 113 LYS cc_start: 0.9359 (ttpp) cc_final: 0.9106 (tppt) REVERT: C 509 MET cc_start: 0.9579 (tpt) cc_final: 0.9313 (tpt) REVERT: C 663 ARG cc_start: 0.8876 (mtm-85) cc_final: 0.8458 (mtm-85) REVERT: B 53 TRP cc_start: 0.6965 (m100) cc_final: 0.6621 (m-10) REVERT: B 281 ASP cc_start: 0.9315 (m-30) cc_final: 0.9039 (m-30) REVERT: B 452 MET cc_start: 0.8595 (mmp) cc_final: 0.8224 (mmm) REVERT: D 68 MET cc_start: 0.6646 (mmm) cc_final: 0.6432 (mmm) REVERT: D 113 LYS cc_start: 0.9367 (ttpp) cc_final: 0.9097 (tppt) REVERT: D 663 ARG cc_start: 0.8864 (mtm-85) cc_final: 0.8444 (mtm-85) REVERT: A 452 MET cc_start: 0.8621 (mmp) cc_final: 0.8245 (mmm) outliers start: 6 outliers final: 8 residues processed: 89 average time/residue: 0.5084 time to fit residues: 51.2349 Evaluate side-chains 91 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain A residue 157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 95 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 106 optimal weight: 0.0870 chunk 178 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.095317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.053472 restraints weight = 45798.791| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.19 r_work: 0.2529 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17944 Z= 0.142 Angle : 0.616 12.665 24456 Z= 0.291 Chirality : 0.043 0.332 2818 Planarity : 0.003 0.042 3012 Dihedral : 8.879 104.146 2742 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.37 % Allowed : 10.59 % Favored : 89.05 % 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 aren not related in a simple way. whole: 1.31 (0.18), residues: 2136 helix: 2.19 (0.16), residues: 1018 sheet: 0.89 (0.42), residues: 160 loop : -0.61 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 663 TYR 0.011 0.001 TYR B 81 PHE 0.026 0.001 PHE A 364 TRP 0.043 0.001 TRP A 98 HIS 0.002 0.001 HIS D 348 Details of bonding type rmsd covalent geometry : bond 0.00320 (17916) covalent geometry : angle 0.59659 (24380) SS BOND : bond 0.00229 ( 8) SS BOND : angle 0.41722 ( 16) hydrogen bonds : bond 0.04116 ( 864) hydrogen bonds : angle 4.04188 ( 2436) link_BETA1-4 : bond 0.01135 ( 10) link_BETA1-4 : angle 3.89342 ( 30) link_NAG-ASN : bond 0.00274 ( 10) link_NAG-ASN : angle 2.21130 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5371.51 seconds wall clock time: 92 minutes 24.98 seconds (5544.98 seconds total)