Starting phenix.real_space_refine on Sun May 18 23:24:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wk6_37596/05_2025/8wk6_37596.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wk6_37596/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wk6_37596/05_2025/8wk6_37596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wk6_37596/05_2025/8wk6_37596.map" model { file = "/net/cci-nas-00/data/ceres_data/8wk6_37596/05_2025/8wk6_37596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wk6_37596/05_2025/8wk6_37596.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.05, per 1000 atoms: 0.58 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: 4.66 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.12 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: 5.42 Time building geometry restraints manager: 5.36 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: 0.00 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: 1.360 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: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 39.120 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.520 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.065 0.002 TRP B 53 HIS 0.002 0.000 HIS D 244 PHE 0.022 0.001 PHE A 364 TYR 0.019 0.001 TYR C 236 ARG 0.007 0.000 ARG D 663 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 10) link_NAG-ASN : angle 2.31619 ( 30) link_BETA1-4 : bond 0.00851 ( 10) link_BETA1-4 : angle 2.62020 ( 30) hydrogen bonds : bond 0.15957 ( 864) hydrogen bonds : angle 5.37642 ( 2436) SS BOND : bond 0.00166 ( 8) SS BOND : angle 0.38169 ( 16) covalent geometry : bond 0.00302 (17916) covalent geometry : angle 0.56101 (24380) *********************** 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 : 2.122 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: 1.1955 time to fit residues: 153.7292 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 : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 194 optimal weight: 0.0050 overall best weight: 2.3198 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.095763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.054237 restraints weight = 45805.130| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.14 r_work: 0.2551 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17944 Z= 0.168 Angle : 0.638 12.789 24456 Z= 0.307 Chirality : 0.046 0.312 2818 Planarity : 0.004 0.053 3012 Dihedral : 16.262 112.320 2742 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.26 % Allowed : 5.56 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 2136 helix: 1.69 (0.17), residues: 1050 sheet: 0.31 (0.44), residues: 146 loop : -0.65 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 53 HIS 0.002 0.001 HIS C 265 PHE 0.022 0.001 PHE A 364 TYR 0.023 0.001 TYR D 236 ARG 0.006 0.000 ARG D 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 10) link_NAG-ASN : angle 2.30132 ( 30) link_BETA1-4 : bond 0.01104 ( 10) link_BETA1-4 : angle 3.27487 ( 30) hydrogen bonds : bond 0.04803 ( 864) hydrogen bonds : angle 4.49244 ( 2436) SS BOND : bond 0.00211 ( 8) SS BOND : angle 0.39599 ( 16) covalent geometry : bond 0.00377 (17916) covalent geometry : angle 0.62327 (24380) *********************** 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 100 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 452 MET cc_start: 0.8715 (mmp) cc_final: 0.8365 (mmm) REVERT: A 452 MET cc_start: 0.8719 (mmp) cc_final: 0.8363 (mmm) outliers start: 5 outliers final: 4 residues processed: 98 average time/residue: 1.3173 time to fit residues: 145.5876 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 : 1.865 ------------------------------------------------------------------------------- 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 157 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 206 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 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 = 0.3721 r_free = 0.3721 target = 0.095887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.054320 restraints weight = 45672.955| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.16 r_work: 0.2555 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17944 Z= 0.141 Angle : 0.606 12.502 24456 Z= 0.288 Chirality : 0.044 0.238 2818 Planarity : 0.004 0.055 3012 Dihedral : 14.697 112.596 2742 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.42 % Allowed : 7.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 2136 helix: 1.85 (0.17), residues: 1038 sheet: 0.40 (0.44), residues: 146 loop : -0.65 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 53 HIS 0.002 0.001 HIS C 244 PHE 0.022 0.001 PHE B 364 TYR 0.015 0.001 TYR C 236 ARG 0.005 0.000 ARG C 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 10) link_NAG-ASN : angle 2.49113 ( 30) link_BETA1-4 : bond 0.01119 ( 10) link_BETA1-4 : angle 3.06671 ( 30) hydrogen bonds : bond 0.04418 ( 864) hydrogen bonds : angle 4.32368 ( 2436) SS BOND : bond 0.00200 ( 8) SS BOND : angle 0.36349 ( 16) covalent geometry : bond 0.00313 (17916) covalent geometry : angle 0.59114 (24380) *********************** 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 96 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 663 ARG cc_start: 0.8875 (mtm-85) cc_final: 0.8630 (mtm-85) REVERT: B 44 MET cc_start: 0.8576 (mpt) cc_final: 0.8358 (mmm) REVERT: B 452 MET cc_start: 0.8701 (mmp) cc_final: 0.8361 (mmm) REVERT: D 663 ARG cc_start: 0.8876 (mtm-85) cc_final: 0.8629 (mtm-85) REVERT: A 452 MET cc_start: 0.8720 (mmp) cc_final: 0.8363 (mmm) outliers start: 8 outliers final: 1 residues processed: 91 average time/residue: 1.2592 time to fit residues: 130.1725 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 : 1.913 ------------------------------------------------------------------------------- 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 89 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 1 optimal weight: 0.0980 chunk 115 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 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 = 0.3719 r_free = 0.3719 target = 0.095637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.054139 restraints weight = 45646.457| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 3.14 r_work: 0.2548 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17944 Z= 0.144 Angle : 0.603 11.403 24456 Z= 0.287 Chirality : 0.043 0.244 2818 Planarity : 0.004 0.057 3012 Dihedral : 13.244 111.664 2742 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.21 % Allowed : 7.86 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.18), residues: 2136 helix: 1.93 (0.17), residues: 1036 sheet: 0.44 (0.44), residues: 146 loop : -0.65 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 53 HIS 0.002 0.001 HIS C 244 PHE 0.023 0.001 PHE B 364 TYR 0.015 0.001 TYR C 236 ARG 0.002 0.000 ARG C 663 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 10) link_NAG-ASN : angle 2.53251 ( 30) link_BETA1-4 : bond 0.01240 ( 10) link_BETA1-4 : angle 3.29115 ( 30) hydrogen bonds : bond 0.04238 ( 864) hydrogen bonds : angle 4.20289 ( 2436) SS BOND : bond 0.00193 ( 8) SS BOND : angle 0.36373 ( 16) covalent geometry : bond 0.00323 (17916) covalent geometry : angle 0.58622 (24380) *********************** 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 121 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 LYS cc_start: 0.9365 (ttpp) cc_final: 0.9050 (tppt) REVERT: B 53 TRP cc_start: 0.6399 (m-10) cc_final: 0.6155 (m-10) REVERT: B 69 GLU cc_start: 0.9105 (tt0) cc_final: 0.8844 (tm-30) REVERT: B 452 MET cc_start: 0.8626 (mmp) cc_final: 0.8298 (mmm) REVERT: D 113 LYS cc_start: 0.9370 (ttpp) cc_final: 0.9051 (tppt) REVERT: A 452 MET cc_start: 0.8690 (mmp) cc_final: 0.8344 (mmm) outliers start: 23 outliers final: 5 residues processed: 113 average time/residue: 1.2034 time to fit residues: 154.1892 Evaluate side-chains 91 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 210 ASP Chi-restraints excluded: chain A residue 157 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 104 optimal weight: 30.0000 chunk 137 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 73 optimal weight: 0.0570 chunk 108 optimal weight: 30.0000 chunk 171 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 overall best weight: 3.0104 ------------------------------------------------------------------------------- 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 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 = 0.3703 r_free = 0.3703 target = 0.094818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.053190 restraints weight = 46254.300| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.15 r_work: 0.2522 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17944 Z= 0.190 Angle : 0.618 11.780 24456 Z= 0.297 Chirality : 0.044 0.256 2818 Planarity : 0.004 0.055 3012 Dihedral : 12.681 111.001 2742 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.73 % Allowed : 9.17 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.18), residues: 2136 helix: 1.97 (0.17), residues: 1038 sheet: 0.47 (0.41), residues: 166 loop : -0.70 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 53 HIS 0.002 0.001 HIS C 348 PHE 0.024 0.001 PHE B 364 TYR 0.012 0.001 TYR D 236 ARG 0.003 0.000 ARG B 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 10) link_NAG-ASN : angle 2.24950 ( 30) link_BETA1-4 : bond 0.01169 ( 10) link_BETA1-4 : angle 3.46338 ( 30) hydrogen bonds : bond 0.04460 ( 864) hydrogen bonds : angle 4.20507 ( 2436) SS BOND : bond 0.00259 ( 8) SS BOND : angle 0.48819 ( 16) covalent geometry : bond 0.00435 (17916) covalent geometry : angle 0.60190 (24380) *********************** 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 100 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 2.148 Fit side-chains revert: symmetry clash REVERT: C 610 MET cc_start: 0.9531 (OUTLIER) cc_final: 0.9327 (mtp) REVERT: C 663 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8664 (mtm-85) REVERT: B 53 TRP cc_start: 0.6570 (m-10) cc_final: 0.6241 (m-10) REVERT: B 452 MET cc_start: 0.8594 (mmp) cc_final: 0.8252 (mmm) REVERT: D 68 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6693 (mmm) REVERT: D 663 ARG cc_start: 0.8874 (mtm-85) cc_final: 0.8653 (mtm-85) REVERT: A 452 MET cc_start: 0.8569 (mmp) cc_final: 0.8237 (mmm) outliers start: 14 outliers final: 2 residues processed: 91 average time/residue: 1.2005 time to fit residues: 124.9449 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 : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 610 MET Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 41 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 209 optimal weight: 20.0000 chunk 23 optimal weight: 0.6980 chunk 182 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 0.0370 overall best weight: 0.5260 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.096792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.054947 restraints weight = 46094.137| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.22 r_work: 0.2574 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17944 Z= 0.104 Angle : 0.594 11.244 24456 Z= 0.278 Chirality : 0.042 0.295 2818 Planarity : 0.004 0.065 3012 Dihedral : 11.772 110.006 2742 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.73 % Allowed : 9.49 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2136 helix: 2.12 (0.16), residues: 1014 sheet: 0.42 (0.44), residues: 146 loop : -0.58 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 98 HIS 0.001 0.000 HIS D 244 PHE 0.021 0.001 PHE B 364 TYR 0.009 0.001 TYR B 81 ARG 0.002 0.000 ARG D 663 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 10) link_NAG-ASN : angle 2.14623 ( 30) link_BETA1-4 : bond 0.01191 ( 10) link_BETA1-4 : angle 3.79240 ( 30) hydrogen bonds : bond 0.03701 ( 864) hydrogen bonds : angle 4.02336 ( 2436) SS BOND : bond 0.00131 ( 8) SS BOND : angle 0.31966 ( 16) covalent geometry : bond 0.00212 (17916) covalent geometry : angle 0.57456 (24380) *********************** 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 105 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 2.054 Fit side-chains revert: symmetry clash REVERT: C 68 MET cc_start: 0.7749 (mtm) cc_final: 0.7544 (mmm) REVERT: C 113 LYS cc_start: 0.9372 (ttpp) cc_final: 0.9101 (tppt) REVERT: B 53 TRP cc_start: 0.6599 (m-10) cc_final: 0.6263 (m-10) REVERT: B 452 MET cc_start: 0.8559 (mmp) cc_final: 0.8235 (mmm) REVERT: D 68 MET cc_start: 0.6726 (mmm) cc_final: 0.6482 (mmm) REVERT: D 113 LYS cc_start: 0.9377 (ttpp) cc_final: 0.9102 (tppt) REVERT: A 452 MET cc_start: 0.8549 (mmp) cc_final: 0.8224 (mmm) outliers start: 14 outliers final: 4 residues processed: 97 average time/residue: 1.2853 time to fit residues: 141.3825 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 : 1.919 ------------------------------------------------------------------------------- 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 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 81 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 176 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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** B 213 GLN A 213 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.093861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.052062 restraints weight = 46098.998| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 3.17 r_work: 0.2490 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 17944 Z= 0.260 Angle : 0.663 11.579 24456 Z= 0.320 Chirality : 0.046 0.313 2818 Planarity : 0.004 0.052 3012 Dihedral : 11.250 108.875 2742 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.42 % Allowed : 9.91 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2136 helix: 2.01 (0.16), residues: 1040 sheet: 0.56 (0.41), residues: 164 loop : -0.66 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 98 HIS 0.003 0.001 HIS D 348 PHE 0.026 0.001 PHE A 364 TYR 0.015 0.001 TYR A 118 ARG 0.003 0.000 ARG C 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 10) link_NAG-ASN : angle 2.18858 ( 30) link_BETA1-4 : bond 0.01127 ( 10) link_BETA1-4 : angle 3.87480 ( 30) hydrogen bonds : bond 0.04909 ( 864) hydrogen bonds : angle 4.23310 ( 2436) SS BOND : bond 0.00355 ( 8) SS BOND : angle 0.62838 ( 16) covalent geometry : bond 0.00605 (17916) covalent geometry : angle 0.64562 (24380) *********************** 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 93 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 TRP cc_start: 0.6732 (m-10) cc_final: 0.6416 (m-10) REVERT: B 281 ASP cc_start: 0.9329 (m-30) cc_final: 0.9086 (m-30) REVERT: B 452 MET cc_start: 0.8597 (mmp) cc_final: 0.8255 (mmm) REVERT: A 452 MET cc_start: 0.8592 (mmp) cc_final: 0.8248 (mmm) outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 1.2254 time to fit residues: 124.5839 Evaluate side-chains 87 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain B residue 157 THR 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 43 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.094249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.052318 restraints weight = 45825.712| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 3.16 r_work: 0.2514 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17944 Z= 0.186 Angle : 0.635 11.736 24456 Z= 0.301 Chirality : 0.045 0.327 2818 Planarity : 0.004 0.049 3012 Dihedral : 10.526 108.285 2742 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.63 % Allowed : 9.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 2136 helix: 2.09 (0.16), residues: 1026 sheet: 0.63 (0.42), residues: 164 loop : -0.63 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 98 HIS 0.003 0.001 HIS C 348 PHE 0.027 0.001 PHE A 364 TYR 0.012 0.001 TYR D 236 ARG 0.006 0.000 ARG D 663 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 10) link_NAG-ASN : angle 2.20826 ( 30) link_BETA1-4 : bond 0.01168 ( 10) link_BETA1-4 : angle 3.86528 ( 30) hydrogen bonds : bond 0.04479 ( 864) hydrogen bonds : angle 4.13287 ( 2436) SS BOND : bond 0.00243 ( 8) SS BOND : angle 0.50261 ( 16) covalent geometry : bond 0.00427 (17916) covalent geometry : angle 0.61610 (24380) *********************** 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 : 1.929 Fit side-chains revert: symmetry clash REVERT: C 68 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6653 (mmm) REVERT: C 113 LYS cc_start: 0.9332 (ttpp) cc_final: 0.9094 (tppt) REVERT: C 663 ARG cc_start: 0.8848 (mtm-85) cc_final: 0.8452 (mtm-85) REVERT: B 53 TRP cc_start: 0.6956 (m-10) cc_final: 0.6556 (m-10) REVERT: B 452 MET cc_start: 0.8598 (mmp) cc_final: 0.8247 (mmm) REVERT: D 113 LYS cc_start: 0.9332 (ttpp) cc_final: 0.9109 (tppt) REVERT: D 663 ARG cc_start: 0.8845 (mtm-85) cc_final: 0.8445 (mtm-85) REVERT: A 452 MET cc_start: 0.8593 (mmp) cc_final: 0.8231 (mmm) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 1.2807 time to fit residues: 131.0844 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 : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 MET 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 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 84 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 194 optimal weight: 0.0170 chunk 123 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.094547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.052580 restraints weight = 45924.757| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 3.17 r_work: 0.2521 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1725 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= 0.162 Angle : 0.628 11.542 24456 Z= 0.295 Chirality : 0.044 0.290 2818 Planarity : 0.004 0.050 3012 Dihedral : 9.779 106.918 2742 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.58 % Allowed : 10.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2136 helix: 2.05 (0.16), residues: 1040 sheet: 0.59 (0.42), residues: 166 loop : -0.67 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 98 HIS 0.002 0.001 HIS D 348 PHE 0.027 0.001 PHE A 364 TYR 0.011 0.001 TYR A 218 ARG 0.005 0.000 ARG D 663 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 10) link_NAG-ASN : angle 2.15129 ( 30) link_BETA1-4 : bond 0.01188 ( 10) link_BETA1-4 : angle 3.94383 ( 30) hydrogen bonds : bond 0.04310 ( 864) hydrogen bonds : angle 4.07211 ( 2436) SS BOND : bond 0.00245 ( 8) SS BOND : angle 0.44066 ( 16) covalent geometry : bond 0.00367 (17916) covalent geometry : angle 0.60884 (24380) *********************** 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 95 residues out of total 1908 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.939 Fit side-chains revert: symmetry clash REVERT: C 68 MET cc_start: 0.6985 (mmm) cc_final: 0.6703 (mmm) REVERT: C 663 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.8452 (mtm-85) REVERT: B 53 TRP cc_start: 0.7002 (m-10) cc_final: 0.6610 (m-10) REVERT: B 452 MET cc_start: 0.8611 (mmp) cc_final: 0.8242 (mmm) REVERT: D 68 MET cc_start: 0.6407 (mmm) cc_final: 0.6081 (mpt) REVERT: D 113 LYS cc_start: 0.9319 (ttpp) cc_final: 0.9076 (tppt) REVERT: D 663 ARG cc_start: 0.8864 (mtm-85) cc_final: 0.8443 (mtm-85) REVERT: A 452 MET cc_start: 0.8610 (mmp) cc_final: 0.8244 (mmm) outliers start: 11 outliers final: 4 residues processed: 93 average time/residue: 1.2599 time to fit residues: 134.1634 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 : 2.100 ------------------------------------------------------------------------------- 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 A residue 157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 170 optimal weight: 0.0000 chunk 67 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.095554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.053879 restraints weight = 45752.397| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.16 r_work: 0.2539 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17944 Z= 0.128 Angle : 0.621 13.972 24456 Z= 0.289 Chirality : 0.043 0.360 2818 Planarity : 0.003 0.044 3012 Dihedral : 9.198 105.437 2742 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.26 % Allowed : 10.48 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 2136 helix: 2.14 (0.16), residues: 1026 sheet: 0.80 (0.42), residues: 162 loop : -0.66 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 98 HIS 0.002 0.001 HIS D 348 PHE 0.025 0.001 PHE B 364 TYR 0.010 0.001 TYR D 236 ARG 0.005 0.000 ARG C 663 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 10) link_NAG-ASN : angle 2.19585 ( 30) link_BETA1-4 : bond 0.01151 ( 10) link_BETA1-4 : angle 3.93610 ( 30) hydrogen bonds : bond 0.03998 ( 864) hydrogen bonds : angle 4.00651 ( 2436) SS BOND : bond 0.00187 ( 8) SS BOND : angle 0.38059 ( 16) covalent geometry : bond 0.00287 (17916) covalent geometry : angle 0.60095 (24380) ********************** 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: 5 poor density : 86 time to evaluate : 1.876 Fit side-chains revert: symmetry clash REVERT: C 68 MET cc_start: 0.6880 (mmm) cc_final: 0.6633 (mmm) REVERT: C 113 LYS cc_start: 0.9374 (ttpp) cc_final: 0.9101 (tppt) REVERT: C 663 ARG cc_start: 0.8861 (mtm-85) cc_final: 0.8435 (mtm-85) REVERT: B 44 MET cc_start: 0.8572 (mmm) cc_final: 0.8335 (mpp) REVERT: B 53 TRP cc_start: 0.6868 (m-10) cc_final: 0.6483 (m-10) REVERT: B 281 ASP cc_start: 0.9308 (m-30) cc_final: 0.9027 (m-30) REVERT: B 452 MET cc_start: 0.8606 (mmp) cc_final: 0.8242 (mmm) REVERT: D 68 MET cc_start: 0.6352 (mmm) cc_final: 0.5996 (mpt) REVERT: D 113 LYS cc_start: 0.9309 (ttpp) cc_final: 0.9070 (tppt) REVERT: D 663 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8426 (mtm-85) REVERT: A 452 MET cc_start: 0.8604 (mmp) cc_final: 0.8244 (mmm) outliers start: 5 outliers final: 5 residues processed: 89 average time/residue: 1.2433 time to fit residues: 125.6427 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 : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 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 A residue 157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 155 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 153 optimal weight: 0.0870 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.096477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.055722 restraints weight = 45427.021| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.12 r_work: 0.2578 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17944 Z= 0.107 Angle : 0.595 13.648 24456 Z= 0.276 Chirality : 0.043 0.346 2818 Planarity : 0.003 0.042 3012 Dihedral : 8.473 102.761 2742 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.21 % Allowed : 10.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 2136 helix: 2.23 (0.17), residues: 1012 sheet: 0.76 (0.44), residues: 142 loop : -0.50 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 98 HIS 0.002 0.000 HIS C 348 PHE 0.023 0.001 PHE B 364 TYR 0.012 0.001 TYR A 218 ARG 0.005 0.000 ARG C 663 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 10) link_NAG-ASN : angle 2.09338 ( 30) link_BETA1-4 : bond 0.01064 ( 10) link_BETA1-4 : angle 3.78645 ( 30) hydrogen bonds : bond 0.03594 ( 864) hydrogen bonds : angle 3.92687 ( 2436) SS BOND : bond 0.00152 ( 8) SS BOND : angle 0.36877 ( 16) covalent geometry : bond 0.00230 (17916) covalent geometry : angle 0.57571 (24380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12036.46 seconds wall clock time: 207 minutes 58.19 seconds (12478.19 seconds total)