Starting phenix.real_space_refine on Sun Aug 24 23:31:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8skv_40568/08_2025/8skv_40568_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8skv_40568/08_2025/8skv_40568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8skv_40568/08_2025/8skv_40568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8skv_40568/08_2025/8skv_40568.map" model { file = "/net/cci-nas-00/data/ceres_data/8skv_40568/08_2025/8skv_40568_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8skv_40568/08_2025/8skv_40568_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.082 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 S 66 5.16 5 C 7695 2.51 5 N 2087 2.21 5 O 2372 1.98 5 H 11341 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23561 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3034 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 7, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3148 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3144 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 80 Chain: "D" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 2978 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 7, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 8095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8095 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 1990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1990 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "a" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 481 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "b" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 481 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" 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: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.44, per 1000 atoms: 0.15 Number of scatterers: 23561 At special positions: 0 Unit cell: (123.5, 114.95, 179.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 2372 8.00 N 2087 7.00 C 7695 6.00 H 11341 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS J 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 299 " - pdb=" SG CYS D 242 " distance=2.04 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS J 15 " distance=2.03 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 323 " distance=2.03 Simple disulfide: pdb=" SG CYS D 369 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 38 " - pdb=" SG CYS E 46 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 239 " - pdb=" SG CYS E 307 " distance=2.03 Simple disulfide: pdb=" SG CYS E 253 " - pdb=" SG CYS E 261 " distance=2.06 Simple disulfide: pdb=" SG CYS E 464 " - pdb=" SG CYS E 526 " distance=2.03 Simple disulfide: pdb=" SG CYS E 478 " - pdb=" SG CYS E 485 " distance=2.03 Simple disulfide: pdb=" SG CYS J 13 " - pdb=" SG CYS J 101 " distance=2.03 Simple disulfide: pdb=" SG CYS J 72 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 109 " - pdb=" SG CYS J 134 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 263 " " NAG B 501 " - " ASN B 263 " " NAG B 502 " - " ASN B 459 " " NAG E 601 " - " ASN E 65 " " NAG E 602 " - " ASN E 481 " " NAG E 603 " - " ASN E 168 " " NAG E 604 " - " ASN E 403 " " NAG G 1 " - " ASN E 72 " " NAG H 1 " - " ASN E 451 " " NAG I 1 " - " ASN C 263 " " NAG O 1 " - " ASN J 49 " Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 494.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 35 sheets defined 13.3% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.762A pdb=" N ASN A 362 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.640A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.932A pdb=" N LEU B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 362' Processing helix chain 'B' and resid 391 through 395 removed outlier: 4.090A pdb=" N TYR B 395 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.597A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 Processing helix chain 'C' and resid 311 through 318 removed outlier: 4.312A pdb=" N TRP C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 421 through 425 Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 391 through 395 removed outlier: 3.990A pdb=" N TYR D 395 " --> pdb=" O ARG D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 427 Processing helix chain 'E' and resid 27 through 33 Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.878A pdb=" N SER E 87 " --> pdb=" O GLN E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 193 through 197 removed outlier: 3.860A pdb=" N ALA E 197 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 246 Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.889A pdb=" N SER E 360 " --> pdb=" O ARG E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 418 removed outlier: 3.892A pdb=" N ALA E 418 " --> pdb=" O SER E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 521 Processing helix chain 'J' and resid 64 through 69 Processing helix chain 'a' and resid 46 through 73 removed outlier: 3.512A pdb=" N LEU a 72 " --> pdb=" O LYS a 68 " (cutoff:3.500A) Processing helix chain 'b' and resid 46 through 73 removed outlier: 3.773A pdb=" N ALA b 50 " --> pdb=" O PRO b 46 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU b 73 " --> pdb=" O ILE b 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 249 removed outlier: 3.577A pdb=" N THR A 265 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 245 through 249 removed outlier: 3.577A pdb=" N THR A 265 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.618A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.618A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA7, first strand: chain 'A' and resid 459 through 462 removed outlier: 6.456A pdb=" N ASN A 459 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL B 462 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N SER A 461 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE J 61 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER B 461 " --> pdb=" O PHE J 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 245 through 249 removed outlier: 3.566A pdb=" N ARG B 245 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 281 Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.602A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.602A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'C' and resid 245 through 249 removed outlier: 3.649A pdb=" N THR C 265 " --> pdb=" O HIS C 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 279 through 280 removed outlier: 3.661A pdb=" N LEU C 334 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 320 through 321 Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 352 removed outlier: 3.743A pdb=" N THR C 368 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AB9, first strand: chain 'D' and resid 459 through 463 removed outlier: 3.786A pdb=" N MET C 464 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS C 457 " --> pdb=" O ARG J 36 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE J 38 " --> pdb=" O HIS C 457 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASN C 459 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE J 40 " --> pdb=" O ASN C 459 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER C 461 " --> pdb=" O ILE J 40 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL J 42 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C 463 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA J 16 " --> pdb=" O ASP J 10 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP J 10 " --> pdb=" O ALA J 16 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE J 18 " --> pdb=" O LEU J 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 245 through 248 removed outlier: 3.576A pdb=" N SER D 306 " --> pdb=" O CYS D 266 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 304 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N CYS D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 278 through 281 Processing sheet with id=AC3, first strand: chain 'D' and resid 348 through 352 removed outlier: 3.592A pdb=" N THR D 368 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 348 through 352 removed outlier: 3.592A pdb=" N THR D 368 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N PHE D 411 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR D 410 " --> pdb=" O GLU D 403 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AC6, first strand: chain 'E' and resid 9 through 13 removed outlier: 3.945A pdb=" N PHE E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY E 93 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR E 36 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG E 39 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 18 through 23 removed outlier: 3.604A pdb=" N THR E 74 " --> pdb=" O PHE E 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 122 through 125 removed outlier: 6.233A pdb=" N TYR E 122 " --> pdb=" O GLN E 218 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU E 220 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL E 124 " --> pdb=" O LEU E 220 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS E 213 " --> pdb=" O CYS E 202 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS E 202 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE E 159 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS E 149 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU E 157 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 130 through 135 removed outlier: 3.739A pdb=" N PHE E 185 " --> pdb=" O CYS E 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 225 through 229 removed outlier: 6.102A pdb=" N ARG E 254 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL E 263 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 234 through 239 Processing sheet with id=AD3, first strand: chain 'E' and resid 340 through 344 removed outlier: 3.697A pdb=" N THR E 433 " --> pdb=" O CYS E 423 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TRP E 366 " --> pdb=" O LEU E 380 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 348 through 354 Processing sheet with id=AD5, first strand: chain 'E' and resid 460 through 462 Processing sheet with id=AD6, first strand: chain 'E' and resid 486 through 487 removed outlier: 3.859A pdb=" N GLN E 486 " --> pdb=" O LYS E 479 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS E 479 " --> pdb=" O GLN E 486 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU E 536 " --> pdb=" O VAL E 528 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLN E 530 " --> pdb=" O TYR E 534 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR E 534 " --> pdb=" O GLN E 530 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 75 through 78 Processing sheet with id=AD8, first strand: chain 'J' and resid 111 through 116 478 hydrogen bonds defined for protein. 1191 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: 4.32 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11336 1.04 - 1.24: 1194 1.24 - 1.43: 4090 1.43 - 1.63: 7137 1.63 - 1.83: 77 Bond restraints: 23834 Sorted by residual: bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 NAG B 502 " pdb=" O5 NAG B 502 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG E 602 " pdb=" O5 NAG E 602 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 23829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 40785 1.19 - 2.38: 1962 2.38 - 3.57: 187 3.57 - 4.75: 27 4.75 - 5.94: 3 Bond angle restraints: 42964 Sorted by residual: angle pdb=" C THR C 282 " pdb=" N PRO C 283 " pdb=" CA PRO C 283 " ideal model delta sigma weight residual 119.84 116.72 3.12 1.25e+00 6.40e-01 6.23e+00 angle pdb=" N SER J 51 " pdb=" CA SER J 51 " pdb=" C SER J 51 " ideal model delta sigma weight residual 108.79 105.54 3.25 1.53e+00 4.27e-01 4.52e+00 angle pdb=" C GLY E 114 " pdb=" N LEU E 115 " pdb=" CA LEU E 115 " ideal model delta sigma weight residual 121.54 125.54 -4.00 1.91e+00 2.74e-01 4.39e+00 angle pdb=" CA GLY E 484 " pdb=" C GLY E 484 " pdb=" N CYS E 485 " ideal model delta sigma weight residual 115.43 117.44 -2.01 9.80e-01 1.04e+00 4.20e+00 angle pdb=" C ILE J 50 " pdb=" N SER J 51 " pdb=" CA SER J 51 " ideal model delta sigma weight residual 121.62 125.36 -3.74 1.83e+00 2.99e-01 4.19e+00 ... (remaining 42959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 10376 17.74 - 35.49: 967 35.49 - 53.23: 300 53.23 - 70.97: 56 70.97 - 88.72: 12 Dihedral angle restraints: 11711 sinusoidal: 6361 harmonic: 5350 Sorted by residual: dihedral pdb=" CB CYS A 299 " pdb=" SG CYS A 299 " pdb=" SG CYS B 242 " pdb=" CB CYS B 242 " ideal model delta sinusoidal sigma weight residual 93.00 165.09 -72.09 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CB CYS E 253 " pdb=" SG CYS E 253 " pdb=" SG CYS E 261 " pdb=" CB CYS E 261 " ideal model delta sinusoidal sigma weight residual 93.00 26.85 66.15 1 1.00e+01 1.00e-02 5.72e+01 dihedral pdb=" CB CYS C 311 " pdb=" SG CYS C 311 " pdb=" SG CYS E 468 " pdb=" CB CYS E 468 " ideal model delta sinusoidal sigma weight residual -86.00 -145.27 59.27 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 11708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1774 0.054 - 0.109: 217 0.109 - 0.163: 63 0.163 - 0.218: 0 0.218 - 0.272: 1 Chirality restraints: 2055 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN E 451 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 5.99e-01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN E 72 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 2052 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 282 " 0.063 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO C 283 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 243 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO C 244 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 244 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 244 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 52 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO J 53 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO J 53 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 53 " -0.023 5.00e-02 4.00e+02 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1358 2.20 - 2.80: 45974 2.80 - 3.40: 56222 3.40 - 4.00: 78167 4.00 - 4.60: 117624 Nonbonded interactions: 299345 Sorted by model distance: nonbonded pdb=" O PRO E 3 " pdb=" HH TYR E 228 " model vdw 1.601 2.450 nonbonded pdb=" O ASN E 505 " pdb=" H ARG E 507 " model vdw 1.610 2.450 nonbonded pdb="HH11 ARG B 346 " pdb=" OH TYR J 135 " model vdw 1.625 2.450 nonbonded pdb=" HD1 HIS E 310 " pdb=" OD1 ASP E 312 " model vdw 1.628 2.450 nonbonded pdb=" O GLU E 359 " pdb=" HG SER E 362 " model vdw 1.633 2.450 ... (remaining 299340 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' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 256 through 421 or (r \ esid 422 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 423 through 425 or (resid 426 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 427 through 445 or (resid 4 \ 46 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 447 through 449 or (resid 450 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 451 through 453 or (resid 454 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 455 through 458 or (resid 459 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or n \ ame HB3 or name HD21)) or resid 460 through 464)) selection = (chain 'B' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 256 through 259 or (r \ esid 260 through 261 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 262 through 345 or (resid 346 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 347 through 356 \ or (resid 357 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 358 through 404 or (resid 405 through 406 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 407 throu \ gh 424 or (resid 425 through 426 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 427 through 449 or (resid 450 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 451 \ through 464)) selection = (chain 'C' and (resid 242 through 310 or (resid 311 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 312 through 345 or (r \ esid 346 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 347 through 356 or (resid 357 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 358 through 424 or (resid 4 \ 25 through 426 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 427 through 449 or (resid 450 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 451 through 453 or (r \ esid 454 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 455 through 458 or (resid 459 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or n \ ame HB2 or name HB3 or name HD21)) or resid 460 through 464)) selection = (chain 'D' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 256 through 262 or (r \ esid 263 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or \ resid 264 through 356 or (resid 357 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 358 through 445 or (resid 446 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 447 through 458 or (resid 459 and (name N or name CA or name C or name O or nam \ e CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name \ HB3 or name HD21)) or resid 460 through 464)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'O' } ncs_group { reference = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.100 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.150 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 0.047 12533 Z= 0.138 Angle : 0.577 5.942 17203 Z= 0.287 Chirality : 0.042 0.272 2055 Planarity : 0.004 0.097 2197 Dihedral : 14.900 88.718 4591 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.04 % Rotamer: Outliers : 0.08 % Allowed : 23.28 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.22), residues: 1612 helix: 1.57 (0.47), residues: 152 sheet: 0.84 (0.21), residues: 630 loop : -1.51 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 416 TYR 0.009 0.001 TYR E 228 PHE 0.015 0.001 PHE E 75 TRP 0.007 0.001 TRP E 366 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00301 (12493) covalent geometry : angle 0.57193 (17108) SS BOND : bond 0.00556 ( 25) SS BOND : angle 1.02218 ( 50) hydrogen bonds : bond 0.14200 ( 428) hydrogen bonds : angle 5.76850 ( 1191) link_BETA1-4 : bond 0.00330 ( 4) link_BETA1-4 : angle 1.72616 ( 12) link_NAG-ASN : bond 0.00215 ( 11) link_NAG-ASN : angle 1.02169 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.420 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.2533 time to fit residues: 27.3015 Evaluate side-chains 76 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN E 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.206522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.160846 restraints weight = 39308.175| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.43 r_work: 0.3393 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.0360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12533 Z= 0.136 Angle : 0.556 5.752 17203 Z= 0.279 Chirality : 0.042 0.169 2055 Planarity : 0.004 0.072 2197 Dihedral : 6.497 59.027 2045 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.28 % Allowed : 23.12 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.22), residues: 1612 helix: 1.60 (0.45), residues: 158 sheet: 0.83 (0.20), residues: 636 loop : -1.62 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 254 TYR 0.010 0.001 TYR E 228 PHE 0.018 0.001 PHE E 75 TRP 0.008 0.001 TRP E 366 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00336 (12493) covalent geometry : angle 0.55226 (17108) SS BOND : bond 0.00266 ( 25) SS BOND : angle 0.97822 ( 50) hydrogen bonds : bond 0.03802 ( 428) hydrogen bonds : angle 5.17124 ( 1191) link_BETA1-4 : bond 0.00298 ( 4) link_BETA1-4 : angle 1.13592 ( 12) link_NAG-ASN : bond 0.00216 ( 11) link_NAG-ASN : angle 1.05786 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.427 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 92 average time/residue: 0.2320 time to fit residues: 30.4289 Evaluate side-chains 90 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 423 CYS Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain J residue 15 CYS Chi-restraints excluded: chain J residue 52 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.206802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.164048 restraints weight = 39314.759| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.28 r_work: 0.3403 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.0528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12533 Z= 0.121 Angle : 0.537 5.634 17203 Z= 0.268 Chirality : 0.041 0.180 2055 Planarity : 0.004 0.064 2197 Dihedral : 6.258 58.919 2045 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.08 % Allowed : 22.16 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.22), residues: 1612 helix: 1.52 (0.45), residues: 160 sheet: 0.84 (0.20), residues: 632 loop : -1.63 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 450 TYR 0.010 0.001 TYR E 228 PHE 0.017 0.001 PHE E 75 TRP 0.008 0.001 TRP E 366 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00305 (12493) covalent geometry : angle 0.53361 (17108) SS BOND : bond 0.00259 ( 25) SS BOND : angle 0.92581 ( 50) hydrogen bonds : bond 0.03404 ( 428) hydrogen bonds : angle 4.91310 ( 1191) link_BETA1-4 : bond 0.00168 ( 4) link_BETA1-4 : angle 1.18039 ( 12) link_NAG-ASN : bond 0.00197 ( 11) link_NAG-ASN : angle 1.03010 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.551 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 19 residues processed: 101 average time/residue: 0.2391 time to fit residues: 34.8113 Evaluate side-chains 96 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 423 CYS Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain J residue 15 CYS Chi-restraints excluded: chain J residue 52 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 8 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.204930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159919 restraints weight = 39237.735| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.39 r_work: 0.3372 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12533 Z= 0.173 Angle : 0.576 5.455 17203 Z= 0.289 Chirality : 0.043 0.180 2055 Planarity : 0.004 0.056 2197 Dihedral : 6.457 59.280 2045 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.64 % Allowed : 21.76 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.22), residues: 1612 helix: 1.61 (0.45), residues: 159 sheet: 0.73 (0.21), residues: 631 loop : -1.65 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 271 TYR 0.013 0.001 TYR E 228 PHE 0.020 0.001 PHE E 75 TRP 0.010 0.001 TRP E 366 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00436 (12493) covalent geometry : angle 0.57118 (17108) SS BOND : bond 0.00353 ( 25) SS BOND : angle 1.04065 ( 50) hydrogen bonds : bond 0.03538 ( 428) hydrogen bonds : angle 4.91615 ( 1191) link_BETA1-4 : bond 0.00091 ( 4) link_BETA1-4 : angle 1.29358 ( 12) link_NAG-ASN : bond 0.00245 ( 11) link_NAG-ASN : angle 1.13458 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8200 (mp) REVERT: A 439 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7106 (mp) REVERT: J 32 ASP cc_start: 0.6093 (t0) cc_final: 0.5883 (t0) REVERT: b 72 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6196 (mp) outliers start: 33 outliers final: 27 residues processed: 104 average time/residue: 0.2676 time to fit residues: 39.4988 Evaluate side-chains 107 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 423 CYS Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain J residue 15 CYS Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain b residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 124 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 16 optimal weight: 0.0050 chunk 53 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 0.0010 chunk 114 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.206487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.161107 restraints weight = 39042.454| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.41 r_work: 0.3382 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12533 Z= 0.114 Angle : 0.533 5.652 17203 Z= 0.266 Chirality : 0.041 0.184 2055 Planarity : 0.004 0.056 2197 Dihedral : 6.223 59.890 2045 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.88 % Allowed : 21.44 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.22), residues: 1612 helix: 1.71 (0.45), residues: 160 sheet: 0.78 (0.21), residues: 631 loop : -1.61 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 450 TYR 0.009 0.001 TYR E 228 PHE 0.016 0.001 PHE E 75 TRP 0.008 0.001 TRP E 366 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00287 (12493) covalent geometry : angle 0.52885 (17108) SS BOND : bond 0.00250 ( 25) SS BOND : angle 0.96134 ( 50) hydrogen bonds : bond 0.03041 ( 428) hydrogen bonds : angle 4.75663 ( 1191) link_BETA1-4 : bond 0.00165 ( 4) link_BETA1-4 : angle 1.18654 ( 12) link_NAG-ASN : bond 0.00201 ( 11) link_NAG-ASN : angle 1.02507 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 439 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7040 (mp) outliers start: 36 outliers final: 30 residues processed: 103 average time/residue: 0.2333 time to fit residues: 35.5594 Evaluate side-chains 108 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 423 CYS Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain J residue 15 CYS Chi-restraints excluded: chain J residue 52 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.206391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.161597 restraints weight = 39428.580| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.42 r_work: 0.3393 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12533 Z= 0.121 Angle : 0.531 5.608 17203 Z= 0.264 Chirality : 0.042 0.183 2055 Planarity : 0.004 0.052 2197 Dihedral : 6.148 59.887 2045 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.88 % Allowed : 21.44 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.22), residues: 1612 helix: 1.73 (0.45), residues: 161 sheet: 0.79 (0.21), residues: 624 loop : -1.56 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 450 TYR 0.010 0.001 TYR E 228 PHE 0.017 0.001 PHE E 75 TRP 0.008 0.001 TRP E 366 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00310 (12493) covalent geometry : angle 0.52742 (17108) SS BOND : bond 0.00232 ( 25) SS BOND : angle 0.86002 ( 50) hydrogen bonds : bond 0.02987 ( 428) hydrogen bonds : angle 4.67629 ( 1191) link_BETA1-4 : bond 0.00153 ( 4) link_BETA1-4 : angle 1.21519 ( 12) link_NAG-ASN : bond 0.00181 ( 11) link_NAG-ASN : angle 1.02259 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 439 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7010 (mp) outliers start: 36 outliers final: 29 residues processed: 107 average time/residue: 0.2422 time to fit residues: 38.0224 Evaluate side-chains 108 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 423 CYS Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 503 ASP Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain J residue 15 CYS Chi-restraints excluded: chain J residue 52 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 0.0570 chunk 147 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.207247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.161943 restraints weight = 39075.809| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.26 r_work: 0.3417 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12533 Z= 0.100 Angle : 0.516 5.706 17203 Z= 0.255 Chirality : 0.041 0.185 2055 Planarity : 0.004 0.049 2197 Dihedral : 5.960 58.350 2045 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.72 % Allowed : 21.04 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.22), residues: 1612 helix: 1.85 (0.45), residues: 161 sheet: 0.82 (0.21), residues: 626 loop : -1.53 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 193 TYR 0.008 0.001 TYR E 228 PHE 0.015 0.001 PHE E 75 TRP 0.007 0.001 TRP E 366 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00252 (12493) covalent geometry : angle 0.51153 (17108) SS BOND : bond 0.00294 ( 25) SS BOND : angle 0.98505 ( 50) hydrogen bonds : bond 0.02745 ( 428) hydrogen bonds : angle 4.55926 ( 1191) link_BETA1-4 : bond 0.00197 ( 4) link_BETA1-4 : angle 1.18355 ( 12) link_NAG-ASN : bond 0.00194 ( 11) link_NAG-ASN : angle 0.97858 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8095 (mp) REVERT: A 439 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7085 (mp) outliers start: 34 outliers final: 27 residues processed: 103 average time/residue: 0.2262 time to fit residues: 34.1299 Evaluate side-chains 104 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 423 CYS Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 503 ASP Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain J residue 15 CYS Chi-restraints excluded: chain J residue 52 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 1.9990 chunk 60 optimal weight: 0.0020 chunk 7 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 30 optimal weight: 30.0000 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.205694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160416 restraints weight = 39266.998| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.42 r_work: 0.3383 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12533 Z= 0.151 Angle : 0.550 5.475 17203 Z= 0.275 Chirality : 0.042 0.185 2055 Planarity : 0.004 0.070 2197 Dihedral : 6.094 57.094 2045 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.88 % Allowed : 20.88 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.22), residues: 1612 helix: 1.76 (0.45), residues: 161 sheet: 0.78 (0.21), residues: 628 loop : -1.60 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 271 TYR 0.013 0.001 TYR E 228 PHE 0.019 0.001 PHE E 75 TRP 0.009 0.001 TRP E 366 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00386 (12493) covalent geometry : angle 0.54571 (17108) SS BOND : bond 0.00304 ( 25) SS BOND : angle 1.04615 ( 50) hydrogen bonds : bond 0.03136 ( 428) hydrogen bonds : angle 4.63312 ( 1191) link_BETA1-4 : bond 0.00090 ( 4) link_BETA1-4 : angle 1.27309 ( 12) link_NAG-ASN : bond 0.00225 ( 11) link_NAG-ASN : angle 1.05614 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8126 (mp) REVERT: A 439 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7027 (mp) outliers start: 36 outliers final: 32 residues processed: 105 average time/residue: 0.2786 time to fit residues: 41.7688 Evaluate side-chains 109 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 423 CYS Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 503 ASP Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain J residue 15 CYS Chi-restraints excluded: chain J residue 52 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 37 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.206402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.161522 restraints weight = 39267.877| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.56 r_work: 0.3388 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12533 Z= 0.118 Angle : 0.529 5.579 17203 Z= 0.263 Chirality : 0.041 0.187 2055 Planarity : 0.004 0.069 2197 Dihedral : 5.957 56.746 2045 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.72 % Allowed : 21.12 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.22), residues: 1612 helix: 1.76 (0.45), residues: 161 sheet: 0.81 (0.21), residues: 623 loop : -1.56 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 450 TYR 0.010 0.001 TYR E 228 PHE 0.017 0.001 PHE E 75 TRP 0.008 0.001 TRP E 366 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00299 (12493) covalent geometry : angle 0.52503 (17108) SS BOND : bond 0.00256 ( 25) SS BOND : angle 0.94235 ( 50) hydrogen bonds : bond 0.02876 ( 428) hydrogen bonds : angle 4.56979 ( 1191) link_BETA1-4 : bond 0.00149 ( 4) link_BETA1-4 : angle 1.20511 ( 12) link_NAG-ASN : bond 0.00196 ( 11) link_NAG-ASN : angle 1.00819 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8131 (mp) REVERT: A 439 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7172 (mp) outliers start: 34 outliers final: 29 residues processed: 103 average time/residue: 0.2565 time to fit residues: 38.4282 Evaluate side-chains 106 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 423 CYS Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 503 ASP Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain J residue 15 CYS Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 118 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 127 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.204942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.156308 restraints weight = 39281.619| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.60 r_work: 0.3398 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12533 Z= 0.104 Angle : 0.513 5.635 17203 Z= 0.254 Chirality : 0.041 0.187 2055 Planarity : 0.004 0.069 2197 Dihedral : 5.721 56.273 2045 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.56 % Allowed : 21.36 % Favored : 76.08 % 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 aren not related in a simple way. whole: -0.31 (0.22), residues: 1612 helix: 1.85 (0.45), residues: 161 sheet: 0.81 (0.21), residues: 633 loop : -1.54 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 450 TYR 0.009 0.001 TYR E 228 PHE 0.016 0.001 PHE E 75 TRP 0.008 0.001 TRP C 281 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00265 (12493) covalent geometry : angle 0.50947 (17108) SS BOND : bond 0.00228 ( 25) SS BOND : angle 0.87591 ( 50) hydrogen bonds : bond 0.02684 ( 428) hydrogen bonds : angle 4.46858 ( 1191) link_BETA1-4 : bond 0.00184 ( 4) link_BETA1-4 : angle 1.18028 ( 12) link_NAG-ASN : bond 0.00171 ( 11) link_NAG-ASN : angle 0.99115 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3224 Ramachandran restraints generated. 1612 Oldfield, 0 Emsley, 1612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 390 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8126 (mp) REVERT: A 439 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7169 (mp) outliers start: 32 outliers final: 28 residues processed: 101 average time/residue: 0.2388 time to fit residues: 35.4709 Evaluate side-chains 105 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 415 SER Chi-restraints excluded: chain E residue 423 CYS Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain E residue 503 ASP Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain J residue 15 CYS Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 154 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.206090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.153253 restraints weight = 38737.102| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.14 r_work: 0.3456 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12533 Z= 0.120 Angle : 0.523 5.578 17203 Z= 0.260 Chirality : 0.041 0.189 2055 Planarity : 0.004 0.065 2197 Dihedral : 5.696 55.897 2045 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.72 % Allowed : 21.20 % Favored : 76.08 % 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 aren not related in a simple way. whole: -0.31 (0.22), residues: 1612 helix: 1.81 (0.45), residues: 161 sheet: 0.83 (0.21), residues: 623 loop : -1.53 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 450 TYR 0.010 0.001 TYR E 228 PHE 0.018 0.001 PHE E 75 TRP 0.008 0.001 TRP E 366 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00308 (12493) covalent geometry : angle 0.51943 (17108) SS BOND : bond 0.00233 ( 25) SS BOND : angle 0.91131 ( 50) hydrogen bonds : bond 0.02797 ( 428) hydrogen bonds : angle 4.47420 ( 1191) link_BETA1-4 : bond 0.00139 ( 4) link_BETA1-4 : angle 1.21286 ( 12) link_NAG-ASN : bond 0.00183 ( 11) link_NAG-ASN : angle 0.99160 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6741.26 seconds wall clock time: 114 minutes 56.38 seconds (6896.38 seconds total)