Starting phenix.real_space_refine on Sat Jul 4 02:08:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wk6_37596/07_2026/8wk6_37596.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wk6_37596/07_2026/8wk6_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_37596/07_2026/8wk6_37596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wk6_37596/07_2026/8wk6_37596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wk6_37596/07_2026/8wk6_37596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wk6_37596/07_2026/8wk6_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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 4.16, per 1000 atoms: 0.24 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: 1.67 Conformation dependent library (CDL) restraints added in 749.1 milliseconds 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: 0.46 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: 2.23 Time building geometry restraints manager: 2.15 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.390 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 are 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/Z covalent geometry : bond 0.00302 / 0.15 (17916) covalent geometry : angle 0.56101 / 0.29 (24380) SS BOND : bond 0.00166 / 0.09 ( 8) SS BOND : angle 0.38169 / 0.24 ( 16) hydrogen bonds : bond 0.15957 / 10.48 ( 864) hydrogen bonds : angle 5.37642 / 3.77 ( 2436) link_BETA1-4 : bond 0.00851 / 0.51 ( 10) link_BETA1-4 : angle 2.62020 / 1.79 ( 30) link_NAG-ASN : bond 0.00460 / 0.30 ( 10) link_NAG-ASN : angle 2.31619 / 1.47 ( 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 : 0.549 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: 0.9257 (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: 0.5424 time to fit residues: 69.5273 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 : 0.559 ------------------------------------------------------------------------------- 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: 7.9990 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... 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 = 0.095814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.054313 restraints weight = 45824.314| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 3.16 r_work: 0.2552 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0877 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= 0.165 Angle : 0.636 12.828 24456 Z= 0.306 Chirality : 0.045 0.263 2818 Planarity : 0.004 0.053 3012 Dihedral : 16.253 112.198 2742 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.26 % Allowed : 5.66 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 2136 helix: 1.70 (0.17), residues: 1050 sheet: 0.31 (0.44), residues: 146 loop : -0.64 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 546 TYR 0.024 0.001 TYR C 236 PHE 0.023 0.001 PHE A 364 TRP 0.050 0.002 TRP B 53 HIS 0.002 0.001 HIS C 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (17916) covalent geometry : angle 0.62195 / 0.30 (24380) SS BOND : bond 0.00213 / 0.10 ( 8) SS BOND : angle 0.41010 / 0.25 ( 16) hydrogen bonds : bond 0.04862 / 3.10 ( 864) hydrogen bonds : angle 4.49130 / 3.16 ( 2436) link_BETA1-4 : bond 0.01114 / 0.73 ( 10) link_BETA1-4 : angle 3.23622 / 2.18 ( 30) link_NAG-ASN : bond 0.00549 / 0.36 ( 10) link_NAG-ASN : angle 2.25128 / 1.37 ( 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 98 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 452 MET cc_start: 0.8714 (mmp) cc_final: 0.8370 (mmm) REVERT: A 452 MET cc_start: 0.8717 (mmp) cc_final: 0.8366 (mmm) outliers start: 5 outliers final: 4 residues processed: 96 average time/residue: 0.6257 time to fit residues: 67.3714 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 : 0.701 ------------------------------------------------------------------------------- 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: 0.8980 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 154 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3732 r_free = 0.3732 target = 0.096455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.054875 restraints weight = 45954.209| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.19 r_work: 0.2570 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17944 Z= 0.122 Angle : 0.597 12.221 24456 Z= 0.283 Chirality : 0.043 0.239 2818 Planarity : 0.004 0.054 3012 Dihedral : 14.492 112.567 2742 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.47 % Allowed : 7.70 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 2136 helix: 1.86 (0.17), residues: 1038 sheet: 0.44 (0.44), residues: 146 loop : -0.60 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 546 TYR 0.014 0.001 TYR C 236 PHE 0.022 0.001 PHE B 364 TRP 0.038 0.001 TRP B 53 HIS 0.002 0.000 HIS D 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (17916) covalent geometry : angle 0.58151 / 0.28 (24380) SS BOND : bond 0.00168 / 0.09 ( 8) SS BOND : angle 0.32443 / 0.21 ( 16) hydrogen bonds : bond 0.04228 / 2.70 ( 864) hydrogen bonds : angle 4.27743 / 3.02 ( 2436) link_BETA1-4 : bond 0.01149 / 0.74 ( 10) link_BETA1-4 : angle 3.07610 / 2.05 ( 30) link_NAG-ASN : bond 0.00411 / 0.27 ( 10) link_NAG-ASN : angle 2.53038 / 1.42 ( 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 98 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 663 ARG cc_start: 0.8885 (mtm-85) cc_final: 0.8639 (mtm-85) REVERT: B 44 MET cc_start: 0.8559 (mpt) cc_final: 0.8335 (mmm) REVERT: B 452 MET cc_start: 0.8699 (mmp) cc_final: 0.8362 (mmm) REVERT: D 663 ARG cc_start: 0.8882 (mtm-85) cc_final: 0.8633 (mtm-85) REVERT: A 452 MET cc_start: 0.8717 (mmp) cc_final: 0.8358 (mmm) outliers start: 9 outliers final: 1 residues processed: 92 average time/residue: 0.5986 time to fit residues: 62.0390 Evaluate side-chains 87 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 143 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 12 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 80 optimal weight: 30.0000 chunk 195 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3728 r_free = 0.3728 target = 0.096183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.054617 restraints weight = 45888.100| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.17 r_work: 0.2560 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17944 Z= 0.129 Angle : 0.595 11.497 24456 Z= 0.281 Chirality : 0.043 0.245 2818 Planarity : 0.004 0.055 3012 Dihedral : 13.252 111.578 2742 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.05 % Allowed : 8.23 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 2136 helix: 1.91 (0.16), residues: 1040 sheet: 0.46 (0.44), residues: 146 loop : -0.58 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 546 TYR 0.013 0.001 TYR D 65 PHE 0.022 0.001 PHE A 364 TRP 0.035 0.001 TRP B 53 HIS 0.002 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (17916) covalent geometry : angle 0.57696 / 0.28 (24380) SS BOND : bond 0.00178 / 0.09 ( 8) SS BOND : angle 0.35017 / 0.22 ( 16) hydrogen bonds : bond 0.04048 / 2.58 ( 864) hydrogen bonds : angle 4.17967 / 2.96 ( 2436) link_BETA1-4 : bond 0.01255 / 0.79 ( 10) link_BETA1-4 : angle 3.29445 / 2.18 ( 30) link_NAG-ASN : bond 0.00387 / 0.25 ( 10) link_NAG-ASN : angle 2.61549 / 1.45 ( 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 112 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 LYS cc_start: 0.9386 (ttpp) cc_final: 0.9081 (tppt) REVERT: C 663 ARG cc_start: 0.8901 (mtm-85) cc_final: 0.8599 (mtm-85) REVERT: B 53 TRP cc_start: 0.6453 (m-10) cc_final: 0.6169 (m-10) REVERT: B 452 MET cc_start: 0.8624 (mmp) cc_final: 0.8292 (mmm) REVERT: D 113 LYS cc_start: 0.9394 (ttpp) cc_final: 0.9084 (tppt) REVERT: D 663 ARG cc_start: 0.8894 (mtm-85) cc_final: 0.8587 (mtm-85) REVERT: A 44 MET cc_start: 0.8570 (mpt) cc_final: 0.8362 (mmm) REVERT: A 273 ASP cc_start: 0.4990 (p0) cc_final: 0.4172 (p0) REVERT: A 452 MET cc_start: 0.8692 (mmp) cc_final: 0.8346 (mmm) outliers start: 20 outliers final: 2 residues processed: 104 average time/residue: 0.5683 time to fit residues: 67.3120 Evaluate side-chains 88 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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: 3.9990 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 176 optimal weight: 30.0000 chunk 81 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3709 r_free = 0.3709 target = 0.095094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.053030 restraints weight = 45702.073| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.18 r_work: 0.2526 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17944 Z= 0.178 Angle : 0.614 11.624 24456 Z= 0.293 Chirality : 0.044 0.264 2818 Planarity : 0.004 0.054 3012 Dihedral : 12.530 110.757 2742 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.84 % Allowed : 8.81 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.18), residues: 2136 helix: 1.99 (0.16), residues: 1040 sheet: 0.53 (0.41), residues: 166 loop : -0.64 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 584 TYR 0.014 0.001 TYR C 236 PHE 0.024 0.001 PHE A 364 TRP 0.031 0.002 TRP B 98 HIS 0.003 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (17916) covalent geometry : angle 0.59689 / 0.29 (24380) SS BOND : bond 0.00257 / 0.13 ( 8) SS BOND : angle 0.46520 / 0.29 ( 16) hydrogen bonds : bond 0.04402 / 2.80 ( 864) hydrogen bonds : angle 4.18845 / 2.96 ( 2436) link_BETA1-4 : bond 0.01165 / 0.76 ( 10) link_BETA1-4 : angle 3.51573 / 2.29 ( 30) link_NAG-ASN : bond 0.00279 / 0.19 ( 10) link_NAG-ASN : angle 2.21472 / 1.31 ( 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: 16 poor density : 88 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: C 663 ARG cc_start: 0.8876 (mtm-85) cc_final: 0.8657 (mtm-85) REVERT: B 53 TRP cc_start: 0.6651 (m-10) cc_final: 0.6371 (m-10) REVERT: B 452 MET cc_start: 0.8599 (mmp) cc_final: 0.8255 (mmm) REVERT: D 663 ARG cc_start: 0.8875 (mtm-85) cc_final: 0.8652 (mtm-85) REVERT: A 452 MET cc_start: 0.8561 (mmp) cc_final: 0.8227 (mmm) outliers start: 16 outliers final: 4 residues processed: 96 average time/residue: 0.6018 time to fit residues: 65.7237 Evaluate side-chains 90 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 185 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.094109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.052195 restraints weight = 45876.824| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.17 r_work: 0.2496 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17944 Z= 0.231 Angle : 0.647 11.703 24456 Z= 0.311 Chirality : 0.045 0.307 2818 Planarity : 0.004 0.063 3012 Dihedral : 11.843 110.025 2742 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.89 % Allowed : 9.12 % 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 are not related in a simple way. whole: 1.15 (0.18), residues: 2136 helix: 2.00 (0.16), residues: 1040 sheet: 0.62 (0.42), residues: 164 loop : -0.65 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 362 TYR 0.014 0.001 TYR D 236 PHE 0.026 0.001 PHE B 364 TRP 0.035 0.002 TRP A 98 HIS 0.003 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (17916) covalent geometry : angle 0.62905 / 0.31 (24380) SS BOND : bond 0.00294 / 0.14 ( 8) SS BOND : angle 0.59116 / 0.38 ( 16) hydrogen bonds : bond 0.04796 / 3.05 ( 864) hydrogen bonds : angle 4.22435 / 2.98 ( 2436) link_BETA1-4 : bond 0.01101 / 0.74 ( 10) link_BETA1-4 : angle 3.81616 / 2.45 ( 30) link_NAG-ASN : bond 0.00223 / 0.15 ( 10) link_NAG-ASN : angle 2.13888 / 1.28 ( 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 102 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 LYS cc_start: 0.9399 (ttpp) cc_final: 0.9130 (tppt) REVERT: B 53 TRP cc_start: 0.6740 (m-10) cc_final: 0.6418 (m-10) REVERT: B 452 MET cc_start: 0.8613 (mmp) cc_final: 0.8264 (mmm) REVERT: D 68 MET cc_start: 0.6758 (mmm) cc_final: 0.6534 (mmm) REVERT: D 113 LYS cc_start: 0.9399 (ttpp) cc_final: 0.9129 (tppt) REVERT: A 452 MET cc_start: 0.8572 (mmp) cc_final: 0.8233 (mmm) outliers start: 17 outliers final: 7 residues processed: 91 average time/residue: 0.5532 time to fit residues: 57.1144 Evaluate side-chains 91 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 MET 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: 3.9990 chunk 45 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 ASN B 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.094718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.052629 restraints weight = 45745.069| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 3.19 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: 0.8598 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17944 Z= 0.160 Angle : 0.614 11.429 24456 Z= 0.292 Chirality : 0.044 0.308 2818 Planarity : 0.004 0.052 3012 Dihedral : 11.080 109.222 2742 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.58 % Allowed : 9.85 % Favored : 89.57 % 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 are not related in a simple way. whole: 1.20 (0.18), residues: 2136 helix: 2.03 (0.16), residues: 1040 sheet: 0.64 (0.42), residues: 164 loop : -0.60 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 663 TYR 0.012 0.001 TYR C 236 PHE 0.026 0.001 PHE A 364 TRP 0.041 0.002 TRP B 98 HIS 0.002 0.001 HIS D 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (17916) covalent geometry : angle 0.59480 / 0.29 (24380) SS BOND : bond 0.00241 / 0.13 ( 8) SS BOND : angle 0.42732 / 0.28 ( 16) hydrogen bonds : bond 0.04334 / 2.76 ( 864) hydrogen bonds : angle 4.11498 / 2.90 ( 2436) link_BETA1-4 : bond 0.01160 / 0.78 ( 10) link_BETA1-4 : angle 3.86205 / 2.52 ( 30) link_NAG-ASN : bond 0.00279 / 0.17 ( 10) link_NAG-ASN : angle 2.17324 / 1.30 ( 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 97 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 509 MET cc_start: 0.9587 (tpt) cc_final: 0.9297 (tpt) REVERT: C 663 ARG cc_start: 0.8881 (mtm-85) cc_final: 0.8480 (mtm-85) REVERT: B 53 TRP cc_start: 0.6827 (m-10) cc_final: 0.6445 (m-10) REVERT: B 452 MET cc_start: 0.8612 (mmp) cc_final: 0.8247 (mmm) REVERT: D 68 MET cc_start: 0.6756 (mmm) cc_final: 0.6553 (mmm) REVERT: D 663 ARG cc_start: 0.8884 (mtm-85) cc_final: 0.8476 (mtm-85) REVERT: A 452 MET cc_start: 0.8573 (mmp) cc_final: 0.8215 (mmm) outliers start: 11 outliers final: 6 residues processed: 92 average time/residue: 0.5643 time to fit residues: 58.8184 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 : 0.680 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 142 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 92 optimal weight: 0.2980 chunk 83 optimal weight: 50.0000 chunk 203 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.094973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.053007 restraints weight = 45637.223| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.18 r_work: 0.2531 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1632 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= 0.139 Angle : 0.617 12.446 24456 Z= 0.290 Chirality : 0.044 0.356 2818 Planarity : 0.003 0.055 3012 Dihedral : 10.467 108.160 2742 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.58 % Allowed : 9.80 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.19), residues: 2136 helix: 2.12 (0.16), residues: 1026 sheet: 0.60 (0.42), residues: 166 loop : -0.58 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 663 TYR 0.011 0.001 TYR A 218 PHE 0.025 0.001 PHE A 364 TRP 0.038 0.001 TRP A 98 HIS 0.004 0.001 HIS C 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (17916) covalent geometry : angle 0.59762 / 0.29 (24380) SS BOND : bond 0.00196 / 0.10 ( 8) SS BOND : angle 0.39514 / 0.26 ( 16) hydrogen bonds : bond 0.04154 / 2.65 ( 864) hydrogen bonds : angle 4.05634 / 2.86 ( 2436) link_BETA1-4 : bond 0.01197 / 0.81 ( 10) link_BETA1-4 : angle 3.89289 / 2.57 ( 30) link_NAG-ASN : bond 0.00303 / 0.19 ( 10) link_NAG-ASN : angle 2.16261 / 1.31 ( 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 96 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 LYS cc_start: 0.9331 (ttpp) cc_final: 0.9081 (tppt) REVERT: C 509 MET cc_start: 0.9576 (tpt) cc_final: 0.9280 (tpt) REVERT: B 53 TRP cc_start: 0.6937 (m-10) cc_final: 0.6562 (m-10) REVERT: B 452 MET cc_start: 0.8611 (mmp) cc_final: 0.8244 (mmm) REVERT: D 113 LYS cc_start: 0.9333 (ttpp) cc_final: 0.9076 (tppt) REVERT: A 452 MET cc_start: 0.8573 (mmp) cc_final: 0.8214 (mmm) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.5059 time to fit residues: 51.8818 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 : 0.685 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 92 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 210 optimal weight: 6.9990 chunk 112 optimal weight: 0.0030 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.096356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.054358 restraints weight = 45994.189| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.25 r_work: 0.2562 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17944 Z= 0.112 Angle : 0.608 12.947 24456 Z= 0.283 Chirality : 0.043 0.345 2818 Planarity : 0.004 0.056 3012 Dihedral : 9.690 106.599 2742 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.47 % Allowed : 10.38 % 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 are not related in a simple way. whole: 1.32 (0.19), residues: 2136 helix: 2.23 (0.16), residues: 1014 sheet: 0.44 (0.45), residues: 150 loop : -0.52 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 663 TYR 0.010 0.001 TYR A 218 PHE 0.024 0.001 PHE A 364 TRP 0.038 0.001 TRP B 98 HIS 0.002 0.000 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (17916) covalent geometry : angle 0.58776 / 0.28 (24380) SS BOND : bond 0.00182 / 0.10 ( 8) SS BOND : angle 0.33006 / 0.21 ( 16) hydrogen bonds : bond 0.03757 / 2.40 ( 864) hydrogen bonds : angle 3.96488 / 2.80 ( 2436) link_BETA1-4 : bond 0.01209 / 0.81 ( 10) link_BETA1-4 : angle 3.96900 / 2.63 ( 30) link_NAG-ASN : bond 0.00354 / 0.21 ( 10) link_NAG-ASN : angle 2.16599 / 1.30 ( 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 97 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 LYS cc_start: 0.9313 (ttpp) cc_final: 0.9077 (tppt) REVERT: C 663 ARG cc_start: 0.8858 (mtm-85) cc_final: 0.8394 (mtm-85) REVERT: B 53 TRP cc_start: 0.6829 (m-10) cc_final: 0.6456 (m-10) REVERT: B 452 MET cc_start: 0.8604 (mmp) cc_final: 0.8244 (mmm) REVERT: D 68 MET cc_start: 0.6328 (mmm) cc_final: 0.6014 (mpt) REVERT: D 113 LYS cc_start: 0.9313 (ttpp) cc_final: 0.9071 (tppt) REVERT: D 663 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8384 (mtm-85) REVERT: A 452 MET cc_start: 0.8563 (mmp) cc_final: 0.8211 (mmm) outliers start: 9 outliers final: 4 residues processed: 95 average time/residue: 0.5849 time to fit residues: 62.6890 Evaluate side-chains 88 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain D residue 98 LEU 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: 8.9990 chunk 175 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 205 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.095020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053104 restraints weight = 45582.226| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.18 r_work: 0.2530 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17944 Z= 0.166 Angle : 0.629 12.522 24456 Z= 0.295 Chirality : 0.044 0.352 2818 Planarity : 0.004 0.056 3012 Dihedral : 9.279 105.211 2742 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.26 % Allowed : 10.74 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 2136 helix: 2.20 (0.17), residues: 1026 sheet: 0.73 (0.42), residues: 166 loop : -0.59 (0.20), residues: 944 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 0.026 0.001 PHE B 364 TRP 0.041 0.002 TRP B 98 HIS 0.003 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (17916) covalent geometry : angle 0.60996 / 0.29 (24380) SS BOND : bond 0.00228 / 0.12 ( 8) SS BOND : angle 0.43817 / 0.28 ( 16) hydrogen bonds : bond 0.04164 / 2.66 ( 864) hydrogen bonds : angle 4.02860 / 2.85 ( 2436) link_BETA1-4 : bond 0.01153 / 0.78 ( 10) link_BETA1-4 : angle 3.94885 / 2.63 ( 30) link_NAG-ASN : bond 0.00262 / 0.17 ( 10) link_NAG-ASN : angle 2.19698 / 1.32 ( 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 90 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 LYS cc_start: 0.9316 (ttpp) cc_final: 0.9102 (tppt) REVERT: C 663 ARG cc_start: 0.8854 (mtm-85) cc_final: 0.8413 (mtm-85) REVERT: B 44 MET cc_start: 0.8656 (mmm) cc_final: 0.8429 (mpp) REVERT: B 53 TRP cc_start: 0.6960 (m-10) cc_final: 0.6577 (m-10) REVERT: B 281 ASP cc_start: 0.9313 (m-30) cc_final: 0.9066 (m-30) REVERT: B 452 MET cc_start: 0.8621 (mmp) cc_final: 0.8248 (mmm) REVERT: D 113 LYS cc_start: 0.9311 (ttpp) cc_final: 0.9093 (tppt) REVERT: D 663 ARG cc_start: 0.8847 (mtm-85) cc_final: 0.8401 (mtm-85) REVERT: A 452 MET cc_start: 0.8610 (mmp) cc_final: 0.8235 (mmm) outliers start: 5 outliers final: 4 residues processed: 89 average time/residue: 0.5730 time to fit residues: 57.7412 Evaluate side-chains 88 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain D residue 98 LEU 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: 9.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 148 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 170 optimal weight: 0.0970 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.096894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.055514 restraints weight = 45522.379| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.18 r_work: 0.2586 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17944 Z= 0.104 Angle : 0.594 13.197 24456 Z= 0.277 Chirality : 0.043 0.338 2818 Planarity : 0.004 0.057 3012 Dihedral : 8.749 103.565 2742 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.10 % Allowed : 10.85 % 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 are not related in a simple way. whole: 1.40 (0.19), residues: 2136 helix: 2.24 (0.16), residues: 1012 sheet: 0.68 (0.44), residues: 146 loop : -0.43 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 663 TYR 0.009 0.001 TYR D 236 PHE 0.023 0.001 PHE A 364 TRP 0.037 0.001 TRP B 98 HIS 0.005 0.000 HIS D 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (17916) covalent geometry : angle 0.57442 / 0.27 (24380) SS BOND : bond 0.00184 / 0.12 ( 8) SS BOND : angle 0.36858 / 0.23 ( 16) hydrogen bonds : bond 0.03564 / 2.28 ( 864) hydrogen bonds : angle 3.90615 / 2.77 ( 2436) link_BETA1-4 : bond 0.01111 / 0.73 ( 10) link_BETA1-4 : angle 3.83699 / 2.57 ( 30) link_NAG-ASN : bond 0.00378 / 0.23 ( 10) link_NAG-ASN : angle 2.13423 / 1.26 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5696.73 seconds wall clock time: 97 minutes 54.13 seconds (5874.13 seconds total)