Starting phenix.real_space_refine on Sun Aug 24 15:24:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x13_32933/08_2025/7x13_32933.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x13_32933/08_2025/7x13_32933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x13_32933/08_2025/7x13_32933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x13_32933/08_2025/7x13_32933.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x13_32933/08_2025/7x13_32933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x13_32933/08_2025/7x13_32933.map" } resolution = 3.7 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= 0.005 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 13495 2.51 5 N 3568 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 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: 21248 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1783 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 18, 'TRANS': 205} Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1775 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain: "C" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1775 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain: "D" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1769 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain: "E" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1769 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain: "F" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1769 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 18, 'TRANS': 203} Chain: "G" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1761 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain: "H" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1775 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain: "I" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1775 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain: "J" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1775 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Chain: "K" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1761 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain: "L" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1761 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Time building chain proxies: 4.65, per 1000 atoms: 0.22 Number of scatterers: 21248 At special positions: 0 Unit cell: (186.15, 175.95, 135.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4080 8.00 N 3568 7.00 C 13495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 321 " distance=2.04 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 425 " distance=2.04 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 425 " distance=2.03 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 425 " distance=2.03 Simple disulfide: pdb=" SG CYS E 261 " - pdb=" SG CYS E 321 " distance=2.04 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 425 " distance=2.03 Simple disulfide: pdb=" SG CYS F 261 " - pdb=" SG CYS F 321 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 425 " distance=2.03 Simple disulfide: pdb=" SG CYS G 261 " - pdb=" SG CYS G 321 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 425 " distance=2.03 Simple disulfide: pdb=" SG CYS H 261 " - pdb=" SG CYS H 321 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 425 " distance=2.03 Simple disulfide: pdb=" SG CYS I 261 " - pdb=" SG CYS I 321 " distance=2.03 Simple disulfide: pdb=" SG CYS I 367 " - pdb=" SG CYS I 425 " distance=2.03 Simple disulfide: pdb=" SG CYS J 261 " - pdb=" SG CYS J 321 " distance=2.04 Simple disulfide: pdb=" SG CYS J 367 " - pdb=" SG CYS J 425 " distance=2.03 Simple disulfide: pdb=" SG CYS K 261 " - pdb=" SG CYS K 321 " distance=2.04 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 425 " distance=2.03 Simple disulfide: pdb=" SG CYS L 261 " - pdb=" SG CYS L 321 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 425 " 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 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 729.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5096 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 67 sheets defined 13.9% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 246 through 252 Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.803A pdb=" N MET A 358 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR A 359 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 432 through 436 removed outlier: 3.714A pdb=" N TYR A 436 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 4.137A pdb=" N MET B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'C' and resid 309 through 315 removed outlier: 3.613A pdb=" N TRP C 313 " --> pdb=" O CYS C 309 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.576A pdb=" N MET C 358 " --> pdb=" O SER C 354 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C 359 " --> pdb=" O ARG C 355 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 360' Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.890A pdb=" N GLN C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 419' Processing helix chain 'C' and resid 432 through 436 removed outlier: 3.604A pdb=" N TYR C 436 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 Processing helix chain 'D' and resid 309 through 315 removed outlier: 3.686A pdb=" N LEU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN D 315 " --> pdb=" O GLN D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 414 through 420 removed outlier: 3.698A pdb=" N GLN D 419 " --> pdb=" O SER D 415 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 436 Processing helix chain 'E' and resid 246 through 252 removed outlier: 4.136A pdb=" N MET E 252 " --> pdb=" O LYS E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 315 removed outlier: 3.732A pdb=" N TRP E 313 " --> pdb=" O CYS E 309 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 359 Processing helix chain 'E' and resid 414 through 420 Processing helix chain 'E' and resid 432 through 436 removed outlier: 3.562A pdb=" N TYR E 436 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 447 removed outlier: 4.395A pdb=" N GLY E 446 " --> pdb=" O ASP E 442 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS E 447 " --> pdb=" O LYS E 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 442 through 447' Processing helix chain 'F' and resid 246 through 252 Processing helix chain 'F' and resid 310 through 316 removed outlier: 3.642A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 360 removed outlier: 3.722A pdb=" N THR F 359 " --> pdb=" O ARG F 355 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 419 removed outlier: 3.697A pdb=" N GLN F 419 " --> pdb=" O SER F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 436 removed outlier: 3.510A pdb=" N TYR F 436 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 446 removed outlier: 3.617A pdb=" N GLY F 446 " --> pdb=" O LYS F 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 252 Processing helix chain 'G' and resid 309 through 316 removed outlier: 3.869A pdb=" N TRP G 313 " --> pdb=" O CYS G 309 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 314 " --> pdb=" O HIS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 360 removed outlier: 3.611A pdb=" N THR G 359 " --> pdb=" O ARG G 355 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS G 360 " --> pdb=" O GLU G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 419 Processing helix chain 'G' and resid 432 through 436 Processing helix chain 'H' and resid 246 through 252 removed outlier: 3.565A pdb=" N MET H 252 " --> pdb=" O LYS H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 316 removed outlier: 3.550A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 359 Processing helix chain 'H' and resid 414 through 420 removed outlier: 4.068A pdb=" N GLY H 420 " --> pdb=" O ARG H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 436 Processing helix chain 'I' and resid 246 through 252 Processing helix chain 'I' and resid 309 through 316 removed outlier: 4.255A pdb=" N GLY I 316 " --> pdb=" O ASP I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 355 through 359 Processing helix chain 'I' and resid 414 through 419 Processing helix chain 'I' and resid 432 through 436 removed outlier: 3.559A pdb=" N TYR I 436 " --> pdb=" O HIS I 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 251 removed outlier: 3.769A pdb=" N THR J 250 " --> pdb=" O LYS J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 309 through 316 Processing helix chain 'J' and resid 355 through 360 removed outlier: 3.935A pdb=" N MET J 358 " --> pdb=" O ARG J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 415 through 420 removed outlier: 4.214A pdb=" N GLN J 419 " --> pdb=" O SER J 415 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY J 420 " --> pdb=" O ARG J 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 415 through 420' Processing helix chain 'J' and resid 432 through 436 Processing helix chain 'K' and resid 246 through 252 removed outlier: 3.875A pdb=" N THR K 250 " --> pdb=" O LYS K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 316 removed outlier: 3.689A pdb=" N GLY K 316 " --> pdb=" O ASP K 312 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 359 Processing helix chain 'K' and resid 414 through 420 removed outlier: 3.672A pdb=" N GLY K 420 " --> pdb=" O ARG K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 436 removed outlier: 3.562A pdb=" N HIS K 435 " --> pdb=" O LEU K 432 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR K 436 " --> pdb=" O HIS K 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 432 through 436' Processing helix chain 'L' and resid 246 through 251 Processing helix chain 'L' and resid 309 through 316 Processing helix chain 'L' and resid 413 through 420 removed outlier: 3.745A pdb=" N GLY L 420 " --> pdb=" O ARG L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 434 No H-bonds generated for 'chain 'L' and resid 432 through 434' Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 242 removed outlier: 3.965A pdb=" N VAL A 262 " --> pdb=" O PHE A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 242 removed outlier: 3.965A pdb=" N VAL A 262 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 299 " --> pdb=" O GLN A 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 283 removed outlier: 3.668A pdb=" N VAL A 323 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A 332 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 351 removed outlier: 3.793A pdb=" N THR A 366 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 351 removed outlier: 3.793A pdb=" N THR A 366 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 382 removed outlier: 4.249A pdb=" N PHE A 423 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 239 through 243 removed outlier: 3.854A pdb=" N PHE B 243 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR B 260 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS B 261 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER B 304 " --> pdb=" O CYS B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AA9, first strand: chain 'B' and resid 293 through 294 removed outlier: 3.737A pdb=" N GLU B 293 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 301 " --> pdb=" O GLU B 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 347 through 351 removed outlier: 3.742A pdb=" N THR B 366 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE B 404 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 377 through 383 Processing sheet with id=AB3, first strand: chain 'C' and resid 239 through 243 removed outlier: 3.545A pdb=" N THR C 260 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 274 through 278 Processing sheet with id=AB5, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AB6, first strand: chain 'C' and resid 347 through 351 removed outlier: 3.818A pdb=" N THR C 366 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE C 404 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 347 through 351 removed outlier: 3.818A pdb=" N THR C 366 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N PHE C 404 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 377 through 382 removed outlier: 3.739A pdb=" N SER C 424 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE C 423 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 239 through 243 removed outlier: 3.608A pdb=" N SER D 239 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR D 260 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 263 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 302 " --> pdb=" O VAL D 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 239 through 243 removed outlier: 3.608A pdb=" N SER D 239 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR D 260 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 282 through 283 Processing sheet with id=AC3, first strand: chain 'D' and resid 347 through 351 removed outlier: 3.635A pdb=" N THR D 366 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 347 through 351 removed outlier: 3.635A pdb=" N THR D 366 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D 405 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL D 397 " --> pdb=" O PHE D 405 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 386 through 388 removed outlier: 4.715A pdb=" N TRP D 381 " --> pdb=" O GLU D 388 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 449 through 450 removed outlier: 7.461A pdb=" N THR D 449 " --> pdb=" O TYR E 451 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 258 through 266 removed outlier: 6.532A pdb=" N TYR E 300 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL E 305 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 288 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 258 through 266 removed outlier: 6.532A pdb=" N TYR E 300 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG E 301 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU E 293 " --> pdb=" O ARG E 301 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 274 through 279 Processing sheet with id=AD1, first strand: chain 'E' and resid 347 through 351 removed outlier: 3.807A pdb=" N THR E 366 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N PHE E 404 " --> pdb=" O GLY E 371 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 362 through 364 Processing sheet with id=AD3, first strand: chain 'E' and resid 386 through 387 Processing sheet with id=AD4, first strand: chain 'F' and resid 239 through 243 removed outlier: 3.660A pdb=" N THR F 260 " --> pdb=" O PHE F 243 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP F 265 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR F 300 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL F 305 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS F 288 " --> pdb=" O VAL F 305 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 239 through 243 removed outlier: 3.660A pdb=" N THR F 260 " --> pdb=" O PHE F 243 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP F 265 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR F 300 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG F 301 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU F 293 " --> pdb=" O ARG F 301 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 282 through 283 Processing sheet with id=AD7, first strand: chain 'F' and resid 347 through 351 removed outlier: 3.575A pdb=" N THR F 366 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHE F 404 " --> pdb=" O GLY F 371 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 386 through 387 Processing sheet with id=AD9, first strand: chain 'G' and resid 239 through 243 removed outlier: 3.704A pdb=" N THR G 260 " --> pdb=" O PHE G 243 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL G 259 " --> pdb=" O LEU G 306 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU G 306 " --> pdb=" O VAL G 259 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS G 261 " --> pdb=" O SER G 304 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER G 304 " --> pdb=" O CYS G 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 282 through 283 Processing sheet with id=AE2, first strand: chain 'G' and resid 293 through 294 Processing sheet with id=AE3, first strand: chain 'G' and resid 347 through 351 Processing sheet with id=AE4, first strand: chain 'G' and resid 347 through 351 removed outlier: 3.537A pdb=" N PHE G 405 " --> pdb=" O VAL G 397 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 386 through 387 Processing sheet with id=AE6, first strand: chain 'H' and resid 239 through 243 removed outlier: 3.629A pdb=" N THR H 260 " --> pdb=" O PHE H 243 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP H 265 " --> pdb=" O TYR H 300 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR H 300 " --> pdb=" O ASP H 265 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 239 through 243 removed outlier: 3.629A pdb=" N THR H 260 " --> pdb=" O PHE H 243 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP H 265 " --> pdb=" O TYR H 300 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR H 300 " --> pdb=" O ASP H 265 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG H 301 " --> pdb=" O GLU H 293 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU H 293 " --> pdb=" O ARG H 301 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 274 through 279 removed outlier: 3.547A pdb=" N VAL H 323 " --> pdb=" O ILE H 332 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE H 332 " --> pdb=" O VAL H 323 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 347 through 351 removed outlier: 3.631A pdb=" N THR H 366 " --> pdb=" O LEU H 351 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE H 404 " --> pdb=" O GLY H 371 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 347 through 351 removed outlier: 3.631A pdb=" N THR H 366 " --> pdb=" O LEU H 351 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N PHE H 404 " --> pdb=" O GLY H 371 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 386 through 387 Processing sheet with id=AF3, first strand: chain 'H' and resid 453 through 454 Processing sheet with id=AF4, first strand: chain 'I' and resid 239 through 243 removed outlier: 4.681A pdb=" N ASP I 265 " --> pdb=" O TYR I 300 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR I 300 " --> pdb=" O ASP I 265 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL I 305 " --> pdb=" O LYS I 288 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 239 through 243 removed outlier: 4.681A pdb=" N ASP I 265 " --> pdb=" O TYR I 300 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR I 300 " --> pdb=" O ASP I 265 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG I 301 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU I 293 " --> pdb=" O ARG I 301 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 282 through 284 removed outlier: 4.209A pdb=" N TRP I 277 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS I 274 " --> pdb=" O SER I 324 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 347 through 351 removed outlier: 3.955A pdb=" N THR I 366 " --> pdb=" O LEU I 351 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY I 371 " --> pdb=" O PHE I 404 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE I 404 " --> pdb=" O GLY I 371 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 378 through 382 removed outlier: 3.637A pdb=" N PHE I 423 " --> pdb=" O LEU I 441 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 239 through 243 removed outlier: 3.576A pdb=" N PHE J 243 " --> pdb=" O THR J 260 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR J 260 " --> pdb=" O PHE J 243 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 282 through 283 Processing sheet with id=AG2, first strand: chain 'J' and resid 347 through 350 removed outlier: 5.290A pdb=" N PHE J 404 " --> pdb=" O GLY J 371 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 347 through 350 removed outlier: 5.290A pdb=" N PHE J 404 " --> pdb=" O GLY J 371 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE J 405 " --> pdb=" O VAL J 397 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 386 through 387 removed outlier: 3.984A pdb=" N ALA J 378 " --> pdb=" O MET J 428 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE J 423 " --> pdb=" O LEU J 441 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS J 425 " --> pdb=" O LYS J 439 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS J 439 " --> pdb=" O CYS J 425 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 239 through 243 removed outlier: 3.635A pdb=" N VAL K 262 " --> pdb=" O PHE K 241 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE K 243 " --> pdb=" O THR K 260 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR K 260 " --> pdb=" O PHE K 243 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 274 through 279 Processing sheet with id=AG7, first strand: chain 'K' and resid 347 through 350 removed outlier: 3.632A pdb=" N GLY K 371 " --> pdb=" O PHE K 404 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE K 404 " --> pdb=" O GLY K 371 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 386 through 387 Processing sheet with id=AG9, first strand: chain 'L' and resid 239 through 243 removed outlier: 4.006A pdb=" N THR L 260 " --> pdb=" O PHE L 243 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR L 300 " --> pdb=" O ASP L 265 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 239 through 243 removed outlier: 4.006A pdb=" N THR L 260 " --> pdb=" O PHE L 243 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR L 300 " --> pdb=" O ASP L 265 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG L 301 " --> pdb=" O GLU L 293 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU L 293 " --> pdb=" O ARG L 301 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 282 through 283 removed outlier: 4.681A pdb=" N TYR L 319 " --> pdb=" O ILE L 336 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE L 336 " --> pdb=" O TYR L 319 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS L 321 " --> pdb=" O LYS L 334 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS L 334 " --> pdb=" O CYS L 321 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL L 323 " --> pdb=" O ILE L 332 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE L 332 " --> pdb=" O VAL L 323 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 347 through 351 removed outlier: 3.914A pdb=" N THR L 366 " --> pdb=" O LEU L 351 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE L 404 " --> pdb=" O GLY L 371 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 386 through 387 removed outlier: 3.575A pdb=" N SER L 383 " --> pdb=" O GLN L 386 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6789 1.34 - 1.46: 4950 1.46 - 1.58: 9935 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 21824 Sorted by residual: bond pdb=" CB PRO A 352 " pdb=" CG PRO A 352 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.04e+00 bond pdb=" CA PHE E 241 " pdb=" CB PHE E 241 " ideal model delta sigma weight residual 1.528 1.564 -0.035 2.61e-02 1.47e+03 1.82e+00 bond pdb=" CG ARG F 255 " pdb=" CD ARG F 255 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" C ARG E 255 " pdb=" N THR E 256 " ideal model delta sigma weight residual 1.327 1.350 -0.023 2.31e-02 1.87e+03 1.02e+00 bond pdb=" CG PRO A 352 " pdb=" CD PRO A 352 " ideal model delta sigma weight residual 1.503 1.536 -0.033 3.40e-02 8.65e+02 9.34e-01 ... (remaining 21819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 29120 1.44 - 2.88: 446 2.88 - 4.32: 100 4.32 - 5.76: 32 5.76 - 7.20: 7 Bond angle restraints: 29705 Sorted by residual: angle pdb=" CA PRO A 352 " pdb=" N PRO A 352 " pdb=" CD PRO A 352 " ideal model delta sigma weight residual 112.00 107.62 4.38 1.40e+00 5.10e-01 9.77e+00 angle pdb=" C HIS H 433 " pdb=" N ASN H 434 " pdb=" CA ASN H 434 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.00e+00 angle pdb=" CA LYS J 246 " pdb=" CB LYS J 246 " pdb=" CG LYS J 246 " ideal model delta sigma weight residual 114.10 119.56 -5.46 2.00e+00 2.50e-01 7.45e+00 angle pdb=" C LYS J 246 " pdb=" CA LYS J 246 " pdb=" CB LYS J 246 " ideal model delta sigma weight residual 109.82 114.31 -4.49 1.65e+00 3.67e-01 7.41e+00 angle pdb=" C SER F 383 " pdb=" N ASN F 384 " pdb=" CA ASN F 384 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.81e+00 ... (remaining 29700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 11973 17.98 - 35.96: 1125 35.96 - 53.94: 190 53.94 - 71.92: 43 71.92 - 89.90: 24 Dihedral angle restraints: 13355 sinusoidal: 5483 harmonic: 7872 Sorted by residual: dihedral pdb=" CB CYS A 261 " pdb=" SG CYS A 261 " pdb=" SG CYS A 321 " pdb=" CB CYS A 321 " ideal model delta sinusoidal sigma weight residual 93.00 154.66 -61.66 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS C 367 " pdb=" SG CYS C 367 " pdb=" SG CYS C 425 " pdb=" CB CYS C 425 " ideal model delta sinusoidal sigma weight residual 93.00 144.49 -51.49 1 1.00e+01 1.00e-02 3.62e+01 dihedral pdb=" CA LYS J 246 " pdb=" C LYS J 246 " pdb=" N PRO J 247 " pdb=" CA PRO J 247 " ideal model delta harmonic sigma weight residual 180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 13352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2310 0.035 - 0.071: 570 0.071 - 0.106: 281 0.106 - 0.142: 102 0.142 - 0.177: 5 Chirality restraints: 3268 Sorted by residual: chirality pdb=" CB ILE G 336 " pdb=" CA ILE G 336 " pdb=" CG1 ILE G 336 " pdb=" CG2 ILE G 336 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE D 377 " pdb=" N ILE D 377 " pdb=" C ILE D 377 " pdb=" CB ILE D 377 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA LYS A 246 " pdb=" N LYS A 246 " pdb=" C LYS A 246 " pdb=" CB LYS A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 3265 not shown) Planarity restraints: 3821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 351 " -0.056 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO A 352 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 352 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 352 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO I 244 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO I 245 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO I 245 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 245 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 256 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO H 257 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 257 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 257 " -0.029 5.00e-02 4.00e+02 ... (remaining 3818 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 368 2.70 - 3.25: 19384 3.25 - 3.80: 31514 3.80 - 4.35: 39765 4.35 - 4.90: 67473 Nonbonded interactions: 158504 Sorted by model distance: nonbonded pdb=" O GLU K 382 " pdb=" OG SER K 424 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR E 436 " pdb=" NE2 GLN E 438 " model vdw 2.157 3.120 nonbonded pdb=" OG1 THR G 256 " pdb=" O VAL G 308 " model vdw 2.227 3.040 nonbonded pdb=" OD2 ASP G 442 " pdb=" OG SER G 444 " model vdw 2.236 3.040 nonbonded pdb=" NH1 ARG E 255 " pdb=" CG2 THR E 256 " model vdw 2.255 3.540 ... (remaining 158499 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 236 through 456) selection = (chain 'B' and resid 236 through 456) selection = (chain 'C' and resid 236 through 456) selection = (chain 'D' and resid 236 through 456) selection = (chain 'E' and resid 236 through 456) selection = (chain 'F' and resid 236 through 456) selection = chain 'G' selection = (chain 'H' and resid 236 through 456) selection = (chain 'I' and resid 236 through 456) selection = (chain 'J' and resid 236 through 456) selection = chain 'K' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.410 Find NCS groups from input model: 0.360 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5392 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 : 0.002 0.087 21848 Z= 0.093 Angle : 0.507 7.200 29753 Z= 0.264 Chirality : 0.042 0.177 3268 Planarity : 0.003 0.083 3821 Dihedral : 14.422 89.902 8187 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.04 % Allowed : 0.12 % Favored : 99.84 % 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: 2.42 (0.16), residues: 2644 helix: 0.57 (0.39), residues: 195 sheet: 2.23 (0.16), residues: 942 loop : 1.51 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG F 255 TYR 0.012 0.001 TYR D 436 PHE 0.020 0.001 PHE L 372 TRP 0.016 0.001 TRP F 277 HIS 0.002 0.000 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00198 (21824) covalent geometry : angle 0.50675 (29705) SS BOND : bond 0.00336 ( 24) SS BOND : angle 0.59951 ( 48) hydrogen bonds : bond 0.13372 ( 677) hydrogen bonds : angle 5.06894 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 0.587 Fit side-chains REVERT: C 277 TRP cc_start: 0.2439 (m100) cc_final: 0.2171 (m-90) REVERT: J 246 LYS cc_start: 0.4112 (pttp) cc_final: 0.3662 (ptpt) REVERT: L 358 MET cc_start: 0.1663 (pmm) cc_final: 0.1346 (pmm) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.1123 time to fit residues: 48.7577 Evaluate side-chains 207 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.0030 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 overall best weight: 3.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS B 429 HIS C 362 GLN C 435 HIS E 433 HIS E 438 GLN F 418 GLN I 361 ASN J 276 ASN J 361 ASN K 315 ASN L 315 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.214256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.191343 restraints weight = 38851.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.188611 restraints weight = 63331.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.186806 restraints weight = 61764.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.185621 restraints weight = 59829.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.184392 restraints weight = 53531.302| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21848 Z= 0.158 Angle : 0.588 7.837 29753 Z= 0.301 Chirality : 0.045 0.181 3268 Planarity : 0.004 0.056 3821 Dihedral : 3.716 23.054 2848 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.21 % Allowed : 7.63 % Favored : 91.16 % 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: 2.22 (0.16), residues: 2644 helix: 0.66 (0.37), residues: 209 sheet: 2.13 (0.16), residues: 953 loop : 1.30 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 255 TYR 0.015 0.001 TYR H 373 PHE 0.021 0.002 PHE J 405 TRP 0.015 0.001 TRP F 277 HIS 0.007 0.001 HIS G 435 Details of bonding type rmsd covalent geometry : bond 0.00375 (21824) covalent geometry : angle 0.58711 (29705) SS BOND : bond 0.00577 ( 24) SS BOND : angle 0.90029 ( 48) hydrogen bonds : bond 0.03285 ( 677) hydrogen bonds : angle 4.44814 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.599 Fit side-chains REVERT: A 373 TYR cc_start: 0.4368 (t80) cc_final: 0.4008 (t80) REVERT: C 277 TRP cc_start: 0.2597 (m100) cc_final: 0.2188 (m-90) REVERT: D 319 TYR cc_start: 0.5095 (m-80) cc_final: 0.4787 (m-80) REVERT: E 358 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7246 (mmp) REVERT: G 252 MET cc_start: 0.5517 (mmm) cc_final: 0.5123 (mmt) REVERT: G 285 HIS cc_start: 0.5362 (m170) cc_final: 0.4889 (m170) REVERT: I 319 TYR cc_start: 0.3253 (m-80) cc_final: 0.2798 (m-80) REVERT: K 358 MET cc_start: 0.4246 (ptt) cc_final: 0.3801 (ptm) REVERT: K 382 GLU cc_start: 0.4916 (mm-30) cc_final: 0.4250 (mm-30) REVERT: L 358 MET cc_start: 0.1810 (pmm) cc_final: 0.1350 (pmm) outliers start: 30 outliers final: 24 residues processed: 237 average time/residue: 0.1225 time to fit residues: 46.2433 Evaluate side-chains 218 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 358 MET Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain J residue 358 MET Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 452 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 169 optimal weight: 5.9990 chunk 70 optimal weight: 30.0000 chunk 129 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 198 optimal weight: 40.0000 chunk 98 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 4 optimal weight: 0.0070 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 GLN F 310 HIS I 310 HIS I 361 ASN J 315 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.213467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.189808 restraints weight = 38992.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.186472 restraints weight = 63555.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.184951 restraints weight = 66906.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.183940 restraints weight = 63031.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.183115 restraints weight = 57557.585| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21848 Z= 0.122 Angle : 0.533 7.194 29753 Z= 0.269 Chirality : 0.043 0.155 3268 Planarity : 0.003 0.042 3821 Dihedral : 3.700 23.836 2848 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.58 % Allowed : 9.98 % Favored : 88.45 % 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: 2.14 (0.16), residues: 2644 helix: 0.57 (0.36), residues: 220 sheet: 2.06 (0.15), residues: 967 loop : 1.27 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 355 TYR 0.024 0.001 TYR J 278 PHE 0.017 0.001 PHE E 275 TRP 0.012 0.001 TRP F 277 HIS 0.005 0.001 HIS L 429 Details of bonding type rmsd covalent geometry : bond 0.00289 (21824) covalent geometry : angle 0.53216 (29705) SS BOND : bond 0.00495 ( 24) SS BOND : angle 0.73884 ( 48) hydrogen bonds : bond 0.03308 ( 677) hydrogen bonds : angle 4.34801 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.686 Fit side-chains REVERT: C 277 TRP cc_start: 0.2575 (m100) cc_final: 0.1982 (m-90) REVERT: D 319 TYR cc_start: 0.5432 (m-80) cc_final: 0.5020 (m-80) REVERT: F 312 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.6339 (p0) REVERT: G 285 HIS cc_start: 0.5594 (m170) cc_final: 0.5204 (m170) REVERT: G 388 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: H 450 LEU cc_start: 0.5374 (tp) cc_final: 0.5170 (mp) REVERT: I 319 TYR cc_start: 0.3149 (m-80) cc_final: 0.2760 (m-80) REVERT: K 382 GLU cc_start: 0.5178 (mm-30) cc_final: 0.3889 (pp20) REVERT: L 358 MET cc_start: 0.1865 (pmm) cc_final: 0.1399 (pmm) outliers start: 39 outliers final: 26 residues processed: 239 average time/residue: 0.1214 time to fit residues: 46.2429 Evaluate side-chains 225 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 312 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 388 GLU Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain H residue 401 ASP Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 452 ASN Chi-restraints excluded: chain L residue 377 ILE Chi-restraints excluded: chain L residue 449 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 148 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 188 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 154 optimal weight: 40.0000 chunk 218 optimal weight: 20.0000 chunk 173 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS D 315 ASN F 362 GLN F 434 ASN G 433 HIS H 434 ASN I 310 HIS I 325 ASN I 361 ASN J 276 ASN J 386 GLN K 435 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.210585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.186490 restraints weight = 39111.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.184521 restraints weight = 67730.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.182516 restraints weight = 60914.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.180910 restraints weight = 61960.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.180495 restraints weight = 53090.556| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21848 Z= 0.169 Angle : 0.601 7.271 29753 Z= 0.309 Chirality : 0.045 0.162 3268 Planarity : 0.004 0.040 3821 Dihedral : 4.142 20.521 2848 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.79 % Allowed : 11.27 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.16), residues: 2644 helix: 0.28 (0.36), residues: 220 sheet: 1.78 (0.15), residues: 993 loop : 1.13 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 255 TYR 0.018 0.002 TYR H 373 PHE 0.019 0.002 PHE J 405 TRP 0.008 0.001 TRP C 417 HIS 0.006 0.001 HIS C 433 Details of bonding type rmsd covalent geometry : bond 0.00399 (21824) covalent geometry : angle 0.60056 (29705) SS BOND : bond 0.00584 ( 24) SS BOND : angle 0.92060 ( 48) hydrogen bonds : bond 0.03540 ( 677) hydrogen bonds : angle 4.60012 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 218 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 285 HIS cc_start: 0.4221 (p90) cc_final: 0.3907 (p-80) REVERT: B 347 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7036 (mp10) REVERT: B 358 MET cc_start: 0.4246 (ptt) cc_final: 0.3837 (ptt) REVERT: C 277 TRP cc_start: 0.2815 (m100) cc_final: 0.2033 (m-90) REVERT: E 252 MET cc_start: 0.4648 (mtt) cc_final: 0.4349 (mtt) REVERT: G 285 HIS cc_start: 0.5742 (m170) cc_final: 0.5497 (m90) REVERT: G 388 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: I 319 TYR cc_start: 0.3325 (m-80) cc_final: 0.2959 (m-80) REVERT: J 357 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.6033 (pt0) REVERT: K 358 MET cc_start: 0.4360 (ptt) cc_final: 0.3880 (ptm) REVERT: K 382 GLU cc_start: 0.5104 (mm-30) cc_final: 0.4074 (mm-30) REVERT: L 358 MET cc_start: 0.2056 (pmm) cc_final: 0.1623 (pmm) outliers start: 69 outliers final: 49 residues processed: 270 average time/residue: 0.1143 time to fit residues: 50.3049 Evaluate side-chains 247 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 435 HIS Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 312 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 388 GLU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain H residue 434 ASN Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 397 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain J residue 276 ASN Chi-restraints excluded: chain J residue 357 GLU Chi-restraints excluded: chain J residue 358 MET Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 452 ASN Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 377 ILE Chi-restraints excluded: chain L residue 449 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 45 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 242 optimal weight: 40.0000 chunk 244 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 8 optimal weight: 40.0000 chunk 72 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 210 optimal weight: 8.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 GLN F 434 ASN H 310 HIS I 310 HIS I 361 ASN K 435 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.209922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.186708 restraints weight = 38729.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.183857 restraints weight = 63887.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.182457 restraints weight = 60355.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.181615 restraints weight = 66211.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.180320 restraints weight = 62829.730| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21848 Z= 0.187 Angle : 0.624 8.343 29753 Z= 0.321 Chirality : 0.046 0.179 3268 Planarity : 0.004 0.045 3821 Dihedral : 4.413 19.717 2848 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.03 % Allowed : 13.69 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.16), residues: 2644 helix: 0.08 (0.35), residues: 224 sheet: 1.57 (0.15), residues: 982 loop : 0.93 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 344 TYR 0.018 0.002 TYR H 373 PHE 0.019 0.002 PHE J 405 TRP 0.012 0.001 TRP A 381 HIS 0.019 0.001 HIS H 433 Details of bonding type rmsd covalent geometry : bond 0.00449 (21824) covalent geometry : angle 0.62366 (29705) SS BOND : bond 0.00612 ( 24) SS BOND : angle 0.90028 ( 48) hydrogen bonds : bond 0.03794 ( 677) hydrogen bonds : angle 4.78881 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 219 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 HIS cc_start: 0.4603 (p90) cc_final: 0.4043 (p-80) REVERT: A 391 TYR cc_start: 0.5742 (t80) cc_final: 0.5361 (t80) REVERT: B 347 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: B 358 MET cc_start: 0.5033 (ptt) cc_final: 0.4679 (ptt) REVERT: G 388 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: H 315 ASN cc_start: 0.6212 (m110) cc_final: 0.5347 (p0) REVERT: H 442 ASP cc_start: 0.6153 (OUTLIER) cc_final: 0.5923 (m-30) REVERT: I 319 TYR cc_start: 0.3506 (m-80) cc_final: 0.3052 (m-80) REVERT: J 246 LYS cc_start: 0.4799 (pptt) cc_final: 0.3661 (tptp) REVERT: J 373 TYR cc_start: 0.4845 (OUTLIER) cc_final: 0.4583 (m-80) REVERT: L 363 VAL cc_start: 0.5687 (t) cc_final: 0.5475 (p) REVERT: L 398 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6370 (tp) REVERT: L 449 THR cc_start: 0.1989 (OUTLIER) cc_final: 0.1675 (t) outliers start: 75 outliers final: 56 residues processed: 276 average time/residue: 0.1080 time to fit residues: 49.0185 Evaluate side-chains 263 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 201 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 312 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 388 GLU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 310 HIS Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain H residue 442 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain J residue 276 ASN Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 358 MET Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 373 TYR Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 452 ASN Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 398 LEU Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 377 ILE Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 449 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 132 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 79 optimal weight: 0.1980 chunk 166 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 241 optimal weight: 20.0000 chunk 243 optimal weight: 5.9990 chunk 191 optimal weight: 0.0020 chunk 10 optimal weight: 30.0000 chunk 131 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 434 ASN H 310 HIS H 434 ASN I 310 HIS I 361 ASN J 276 ASN ** L 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.210304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.189055 restraints weight = 39003.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.185486 restraints weight = 59810.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.183737 restraints weight = 58144.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.182704 restraints weight = 56808.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.181241 restraints weight = 56572.378| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21848 Z= 0.116 Angle : 0.567 9.550 29753 Z= 0.286 Chirality : 0.045 0.200 3268 Planarity : 0.003 0.043 3821 Dihedral : 4.189 18.935 2848 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.67 % Allowed : 15.15 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.16), residues: 2644 helix: 0.20 (0.36), residues: 224 sheet: 1.63 (0.15), residues: 983 loop : 1.00 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 255 TYR 0.015 0.001 TYR G 373 PHE 0.021 0.001 PHE J 405 TRP 0.007 0.001 TRP F 277 HIS 0.004 0.001 HIS H 310 Details of bonding type rmsd covalent geometry : bond 0.00275 (21824) covalent geometry : angle 0.56643 (29705) SS BOND : bond 0.00518 ( 24) SS BOND : angle 0.76361 ( 48) hydrogen bonds : bond 0.03245 ( 677) hydrogen bonds : angle 4.56397 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 285 HIS cc_start: 0.4429 (p90) cc_final: 0.4019 (p-80) REVERT: B 358 MET cc_start: 0.4841 (ptt) cc_final: 0.4599 (ptt) REVERT: C 252 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.4643 (mtt) REVERT: F 449 THR cc_start: 0.1916 (OUTLIER) cc_final: 0.1517 (m) REVERT: G 388 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: G 437 THR cc_start: 0.8586 (m) cc_final: 0.8353 (m) REVERT: H 442 ASP cc_start: 0.6172 (OUTLIER) cc_final: 0.5892 (p0) REVERT: J 246 LYS cc_start: 0.4821 (pptt) cc_final: 0.3738 (tptp) REVERT: J 373 TYR cc_start: 0.5142 (OUTLIER) cc_final: 0.4862 (m-80) REVERT: L 398 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6451 (tp) REVERT: L 449 THR cc_start: 0.1862 (p) cc_final: 0.1568 (t) outliers start: 66 outliers final: 47 residues processed: 267 average time/residue: 0.1076 time to fit residues: 46.8046 Evaluate side-chains 254 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 201 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 424 SER Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 359 THR Chi-restraints excluded: chain G residue 388 GLU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 310 HIS Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain H residue 442 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 373 TYR Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 452 ASN Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain K residue 398 LEU Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 398 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 259 optimal weight: 7.9990 chunk 94 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 390 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 310 HIS H 434 ASN I 310 HIS I 361 ASN J 276 ASN K 435 HIS ** L 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.207929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.185803 restraints weight = 38797.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.181646 restraints weight = 57314.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.180331 restraints weight = 58690.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.179086 restraints weight = 57120.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.177350 restraints weight = 60676.334| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21848 Z= 0.190 Angle : 0.648 9.610 29753 Z= 0.332 Chirality : 0.046 0.175 3268 Planarity : 0.004 0.043 3821 Dihedral : 4.583 19.566 2848 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.39 % Allowed : 15.59 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.16), residues: 2644 helix: -0.10 (0.35), residues: 225 sheet: 1.38 (0.15), residues: 964 loop : 0.81 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 255 TYR 0.018 0.002 TYR H 373 PHE 0.020 0.002 PHE J 405 TRP 0.013 0.001 TRP I 313 HIS 0.036 0.001 HIS H 310 Details of bonding type rmsd covalent geometry : bond 0.00458 (21824) covalent geometry : angle 0.64761 (29705) SS BOND : bond 0.00604 ( 24) SS BOND : angle 0.99522 ( 48) hydrogen bonds : bond 0.03764 ( 677) hydrogen bonds : angle 4.84368 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 209 time to evaluate : 0.510 Fit side-chains REVERT: A 285 HIS cc_start: 0.4470 (p90) cc_final: 0.4028 (p-80) REVERT: B 252 MET cc_start: 0.4076 (ppp) cc_final: 0.3833 (ppp) REVERT: B 347 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7010 (mp10) REVERT: F 312 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6387 (p0) REVERT: F 449 THR cc_start: 0.2166 (OUTLIER) cc_final: 0.1810 (m) REVERT: G 388 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: G 437 THR cc_start: 0.8552 (m) cc_final: 0.8349 (m) REVERT: H 442 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.5921 (p0) REVERT: J 246 LYS cc_start: 0.4946 (pptt) cc_final: 0.3798 (tptp) REVERT: L 398 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6413 (tp) REVERT: L 449 THR cc_start: 0.2218 (OUTLIER) cc_final: 0.1885 (t) outliers start: 84 outliers final: 65 residues processed: 271 average time/residue: 0.1054 time to fit residues: 46.5822 Evaluate side-chains 276 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 204 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 347 GLN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 312 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 424 SER Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 359 THR Chi-restraints excluded: chain G residue 388 GLU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain H residue 434 ASN Chi-restraints excluded: chain H residue 442 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 358 MET Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain J residue 452 ASN Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain K residue 412 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 377 ILE Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 449 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 111 optimal weight: 9.9990 chunk 180 optimal weight: 20.0000 chunk 4 optimal weight: 0.0670 chunk 198 optimal weight: 20.0000 chunk 109 optimal weight: 0.3980 chunk 262 optimal weight: 20.0000 chunk 239 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 56 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 overall best weight: 2.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN H 310 HIS H 434 ASN I 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.209571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.186967 restraints weight = 38455.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.183839 restraints weight = 60694.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.181942 restraints weight = 57403.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.181297 restraints weight = 57394.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.180285 restraints weight = 45842.170| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21848 Z= 0.118 Angle : 0.581 8.455 29753 Z= 0.294 Chirality : 0.044 0.185 3268 Planarity : 0.004 0.042 3821 Dihedral : 4.293 18.307 2848 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.87 % Allowed : 16.32 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.16), residues: 2644 helix: 0.08 (0.36), residues: 225 sheet: 1.49 (0.15), residues: 975 loop : 0.89 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 344 TYR 0.014 0.001 TYR G 373 PHE 0.021 0.001 PHE J 405 TRP 0.008 0.001 TRP E 277 HIS 0.009 0.001 HIS H 433 Details of bonding type rmsd covalent geometry : bond 0.00278 (21824) covalent geometry : angle 0.58015 (29705) SS BOND : bond 0.00513 ( 24) SS BOND : angle 0.77841 ( 48) hydrogen bonds : bond 0.03234 ( 677) hydrogen bonds : angle 4.61126 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 210 time to evaluate : 0.798 Fit side-chains REVERT: A 285 HIS cc_start: 0.4515 (p90) cc_final: 0.3982 (p-80) REVERT: A 391 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.6004 (t80) REVERT: C 252 MET cc_start: 0.5750 (OUTLIER) cc_final: 0.4684 (mtt) REVERT: F 284 VAL cc_start: 0.3515 (OUTLIER) cc_final: 0.3235 (p) REVERT: F 449 THR cc_start: 0.2301 (OUTLIER) cc_final: 0.1930 (m) REVERT: G 388 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: G 437 THR cc_start: 0.8610 (m) cc_final: 0.8376 (m) REVERT: H 442 ASP cc_start: 0.6266 (OUTLIER) cc_final: 0.5990 (p0) REVERT: J 246 LYS cc_start: 0.4971 (pptt) cc_final: 0.3885 (tptp) REVERT: L 398 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6424 (tp) REVERT: L 449 THR cc_start: 0.2198 (p) cc_final: 0.1806 (t) outliers start: 71 outliers final: 54 residues processed: 262 average time/residue: 0.1032 time to fit residues: 44.3152 Evaluate side-chains 262 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 201 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 424 SER Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 359 THR Chi-restraints excluded: chain G residue 388 GLU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 310 HIS Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain H residue 434 ASN Chi-restraints excluded: chain H residue 442 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain J residue 276 ASN Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 358 MET Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain K residue 412 VAL Chi-restraints excluded: chain L residue 397 VAL Chi-restraints excluded: chain L residue 398 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 154 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 119 optimal weight: 0.0040 chunk 121 optimal weight: 0.0170 chunk 60 optimal weight: 0.3980 chunk 176 optimal weight: 30.0000 overall best weight: 2.0834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN H 310 HIS H 434 ASN I 361 ASN L 315 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.209829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.186900 restraints weight = 38545.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.183601 restraints weight = 61338.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.181852 restraints weight = 58712.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.180830 restraints weight = 61871.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.179165 restraints weight = 56835.611| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21848 Z= 0.111 Angle : 0.577 8.737 29753 Z= 0.291 Chirality : 0.044 0.163 3268 Planarity : 0.004 0.041 3821 Dihedral : 4.209 19.223 2848 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.54 % Allowed : 16.76 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.16), residues: 2644 helix: 0.15 (0.36), residues: 225 sheet: 1.56 (0.15), residues: 971 loop : 0.93 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 344 TYR 0.014 0.001 TYR A 391 PHE 0.021 0.001 PHE J 405 TRP 0.009 0.001 TRP C 277 HIS 0.011 0.001 HIS H 310 Details of bonding type rmsd covalent geometry : bond 0.00265 (21824) covalent geometry : angle 0.57705 (29705) SS BOND : bond 0.00467 ( 24) SS BOND : angle 0.74416 ( 48) hydrogen bonds : bond 0.03152 ( 677) hydrogen bonds : angle 4.54540 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 0.565 Fit side-chains REVERT: A 285 HIS cc_start: 0.4571 (p90) cc_final: 0.4080 (p-80) REVERT: A 391 TYR cc_start: 0.6276 (OUTLIER) cc_final: 0.6018 (t80) REVERT: C 252 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.4785 (mtt) REVERT: D 319 TYR cc_start: 0.5662 (m-80) cc_final: 0.4988 (m-80) REVERT: E 283 GLU cc_start: 0.6674 (tp30) cc_final: 0.6145 (mm-30) REVERT: F 284 VAL cc_start: 0.3525 (OUTLIER) cc_final: 0.3243 (p) REVERT: F 312 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6357 (p0) REVERT: G 388 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6460 (mp0) REVERT: G 437 THR cc_start: 0.8619 (m) cc_final: 0.8383 (m) REVERT: H 315 ASN cc_start: 0.6312 (m110) cc_final: 0.5854 (t0) REVERT: J 246 LYS cc_start: 0.4890 (pptt) cc_final: 0.3819 (tptp) REVERT: L 449 THR cc_start: 0.2308 (p) cc_final: 0.1890 (t) outliers start: 63 outliers final: 51 residues processed: 256 average time/residue: 0.1029 time to fit residues: 42.8723 Evaluate side-chains 259 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 203 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 312 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 424 SER Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 359 THR Chi-restraints excluded: chain G residue 388 GLU Chi-restraints excluded: chain G residue 394 THR Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 310 HIS Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain H residue 434 ASN Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain J residue 276 ASN Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 358 MET Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain K residue 412 VAL Chi-restraints excluded: chain L residue 397 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 99 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 55 optimal weight: 0.0870 chunk 8 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 434 ASN H 310 HIS H 434 ASN I 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.211339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.188645 restraints weight = 38542.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.186047 restraints weight = 62710.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.184356 restraints weight = 51694.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.183293 restraints weight = 53197.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.182722 restraints weight = 50539.082| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21848 Z= 0.098 Angle : 0.567 12.276 29753 Z= 0.284 Chirality : 0.044 0.207 3268 Planarity : 0.004 0.048 3821 Dihedral : 4.025 25.164 2848 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.62 % Allowed : 17.85 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.16), residues: 2644 helix: 0.20 (0.37), residues: 225 sheet: 1.65 (0.16), residues: 971 loop : 1.05 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 344 TYR 0.016 0.001 TYR A 391 PHE 0.022 0.001 PHE J 405 TRP 0.011 0.001 TRP F 277 HIS 0.009 0.000 HIS H 433 Details of bonding type rmsd covalent geometry : bond 0.00220 (21824) covalent geometry : angle 0.56721 (29705) SS BOND : bond 0.00399 ( 24) SS BOND : angle 0.67092 ( 48) hydrogen bonds : bond 0.02870 ( 677) hydrogen bonds : angle 4.37803 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.531 Fit side-chains REVERT: A 285 HIS cc_start: 0.4563 (p90) cc_final: 0.4026 (p-80) REVERT: D 319 TYR cc_start: 0.5707 (m-80) cc_final: 0.5048 (m-80) REVERT: E 283 GLU cc_start: 0.6634 (tp30) cc_final: 0.6135 (mm-30) REVERT: F 284 VAL cc_start: 0.3344 (OUTLIER) cc_final: 0.3076 (p) REVERT: F 312 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.6253 (p0) REVERT: G 388 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: G 437 THR cc_start: 0.8628 (m) cc_final: 0.8400 (m) REVERT: H 315 ASN cc_start: 0.6192 (m110) cc_final: 0.5803 (t0) REVERT: J 246 LYS cc_start: 0.4774 (pptt) cc_final: 0.3804 (tptp) REVERT: L 429 HIS cc_start: 0.6434 (t-90) cc_final: 0.6038 (t-170) REVERT: L 449 THR cc_start: 0.2317 (p) cc_final: 0.1893 (t) outliers start: 40 outliers final: 33 residues processed: 240 average time/residue: 0.1095 time to fit residues: 42.2441 Evaluate side-chains 241 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 312 ASP Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain G residue 388 GLU Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain H residue 310 HIS Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 434 ASN Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 368 LEU Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 428 MET Chi-restraints excluded: chain J residue 276 ASN Chi-restraints excluded: chain J residue 358 MET Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 411 THR Chi-restraints excluded: chain K residue 323 VAL Chi-restraints excluded: chain K residue 412 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 238 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 237 optimal weight: 7.9990 chunk 195 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 55 optimal weight: 0.0060 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 434 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 310 HIS H 434 ASN I 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.211606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.189166 restraints weight = 38712.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.185594 restraints weight = 62238.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.184597 restraints weight = 58443.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.183232 restraints weight = 55592.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.182218 restraints weight = 58447.602| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21848 Z= 0.092 Angle : 0.556 9.409 29753 Z= 0.276 Chirality : 0.043 0.146 3268 Planarity : 0.004 0.043 3821 Dihedral : 3.922 18.551 2848 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.70 % Allowed : 17.85 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.16), residues: 2644 helix: 0.20 (0.37), residues: 226 sheet: 1.69 (0.16), residues: 973 loop : 1.12 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 344 TYR 0.017 0.001 TYR A 391 PHE 0.022 0.001 PHE J 405 TRP 0.011 0.001 TRP F 277 HIS 0.006 0.000 HIS H 310 Details of bonding type rmsd covalent geometry : bond 0.00215 (21824) covalent geometry : angle 0.55583 (29705) SS BOND : bond 0.00393 ( 24) SS BOND : angle 0.66176 ( 48) hydrogen bonds : bond 0.02799 ( 677) hydrogen bonds : angle 4.30537 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.37 seconds wall clock time: 46 minutes 27.22 seconds (2787.22 seconds total)