Starting phenix.real_space_refine on Wed May 21 04:30:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x13_32933/05_2025/7x13_32933.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x13_32933/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x13_32933/05_2025/7x13_32933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x13_32933/05_2025/7x13_32933.map" model { file = "/net/cci-nas-00/data/ceres_data/7x13_32933/05_2025/7x13_32933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x13_32933/05_2025/7x13_32933.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.68, per 1000 atoms: 0.64 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: 4.57 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 3.49 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: 7.68 Time building geometry restraints manager: 5.43 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: 0.620 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 47.390 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.120 ------------------------------------------------------------------------------- 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 : 8.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.016 0.001 TRP F 277 HIS 0.002 0.000 HIS A 429 PHE 0.020 0.001 PHE L 372 TYR 0.012 0.001 TYR D 436 ARG 0.019 0.000 ARG F 255 Details of bonding type rmsd hydrogen bonds : bond 0.13372 ( 677) hydrogen bonds : angle 5.06894 ( 2046) SS BOND : bond 0.00336 ( 24) SS BOND : angle 0.59951 ( 48) covalent geometry : bond 0.00198 (21824) covalent geometry : angle 0.50675 (29705) *********************** 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 : 2.185 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: 0.2932 time to fit residues: 125.4791 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 : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 40.0000 chunk 200 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 154 optimal weight: 50.0000 chunk 239 optimal weight: 0.0010 overall best weight: 5.1994 ------------------------------------------------------------------------------- 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 390 ASN C 435 HIS E 433 HIS E 438 GLN F 310 HIS F 418 GLN F 419 GLN I 310 HIS I 361 ASN J 276 ASN J 361 ASN ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 435 HIS L 315 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.211977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.189478 restraints weight = 38721.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.186514 restraints weight = 67900.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.184472 restraints weight = 62856.089| |-----------------------------------------------------------------------------| r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21848 Z= 0.205 Angle : 0.655 9.102 29753 Z= 0.337 Chirality : 0.047 0.170 3268 Planarity : 0.004 0.065 3821 Dihedral : 4.130 22.470 2848 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.45 % Allowed : 8.32 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.16), residues: 2644 helix: 0.29 (0.35), residues: 215 sheet: 1.98 (0.15), residues: 980 loop : 1.19 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 277 HIS 0.009 0.002 HIS G 435 PHE 0.020 0.002 PHE E 275 TYR 0.021 0.002 TYR H 373 ARG 0.008 0.001 ARG D 255 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 677) hydrogen bonds : angle 4.67869 ( 2046) SS BOND : bond 0.00976 ( 24) SS BOND : angle 1.15006 ( 48) covalent geometry : bond 0.00490 (21824) covalent geometry : angle 0.65382 (29705) *********************** 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 252 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 2.614 Fit side-chains REVERT: C 277 TRP cc_start: 0.2498 (m100) cc_final: 0.2080 (m-90) REVERT: D 319 TYR cc_start: 0.5155 (m-80) cc_final: 0.4760 (m-80) REVERT: G 252 MET cc_start: 0.5510 (mmm) cc_final: 0.5161 (mmt) REVERT: G 285 HIS cc_start: 0.5596 (m170) cc_final: 0.5142 (m170) REVERT: H 315 ASN cc_start: 0.5572 (m110) cc_final: 0.5308 (p0) REVERT: I 319 TYR cc_start: 0.3238 (m-80) cc_final: 0.2815 (m-80) REVERT: J 246 LYS cc_start: 0.3875 (pttp) cc_final: 0.3506 (ptpt) REVERT: K 382 GLU cc_start: 0.4610 (mm-30) cc_final: 0.3900 (mm-30) REVERT: L 358 MET cc_start: 0.1818 (pmm) cc_final: 0.1341 (pmm) outliers start: 36 outliers final: 28 residues processed: 241 average time/residue: 0.3067 time to fit residues: 117.8473 Evaluate side-chains 218 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 2.250 ------------------------------------------------------------------------------- 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 252 MET 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 422 VAL Chi-restraints excluded: chain C residue 427 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 366 THR 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 394 THR Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 430 GLU 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 Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain L residue 377 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 163 optimal weight: 30.0000 chunk 169 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS H 310 HIS I 361 ASN K 315 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.213395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.189335 restraints weight = 38378.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.186795 restraints weight = 65588.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.185058 restraints weight = 63291.057| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5879 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21848 Z= 0.104 Angle : 0.527 7.536 29753 Z= 0.265 Chirality : 0.043 0.156 3268 Planarity : 0.003 0.046 3821 Dihedral : 3.731 20.297 2848 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.25 % Allowed : 10.62 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.16), residues: 2644 helix: 0.61 (0.37), residues: 215 sheet: 2.00 (0.15), residues: 963 loop : 1.27 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 277 HIS 0.007 0.001 HIS A 285 PHE 0.022 0.001 PHE J 405 TYR 0.012 0.001 TYR G 373 ARG 0.003 0.000 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 677) hydrogen bonds : angle 4.37220 ( 2046) SS BOND : bond 0.00456 ( 24) SS BOND : angle 0.68662 ( 48) covalent geometry : bond 0.00245 (21824) covalent geometry : angle 0.52653 (29705) *********************** 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 244 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 2.234 Fit side-chains REVERT: A 285 HIS cc_start: 0.4165 (p90) cc_final: 0.3905 (p-80) REVERT: C 277 TRP cc_start: 0.2537 (m100) cc_final: 0.1958 (m-90) REVERT: D 319 TYR cc_start: 0.5381 (m-80) cc_final: 0.4949 (m-80) REVERT: D 437 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8820 (m) REVERT: G 285 HIS cc_start: 0.5574 (m170) cc_final: 0.5163 (m170) REVERT: I 319 TYR cc_start: 0.3268 (m-80) cc_final: 0.2850 (m-80) REVERT: J 246 LYS cc_start: 0.3748 (pttp) cc_final: 0.3525 (ptpt) REVERT: K 382 GLU cc_start: 0.5037 (mm-30) cc_final: 0.4215 (mm-30) REVERT: L 358 MET cc_start: 0.1884 (pmm) cc_final: 0.1359 (pmm) outliers start: 31 outliers final: 23 residues processed: 234 average time/residue: 0.2915 time to fit residues: 110.3131 Evaluate side-chains 217 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 437 THR 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 376 ASP Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain H residue 310 HIS Chi-restraints excluded: chain H residue 369 VAL 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 K residue 279 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 29 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 362 GLN F 434 ASN G 433 HIS H 310 HIS I 310 HIS I 361 ASN J 315 ASN ** L 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 434 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.211952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.188093 restraints weight = 38738.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.184922 restraints weight = 64441.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.183185 restraints weight = 62191.412| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21848 Z= 0.124 Angle : 0.546 7.447 29753 Z= 0.277 Chirality : 0.044 0.155 3268 Planarity : 0.003 0.045 3821 Dihedral : 3.815 18.709 2848 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.06 % Allowed : 11.67 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.16), residues: 2644 helix: 0.57 (0.37), residues: 215 sheet: 1.88 (0.15), residues: 989 loop : 1.24 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 277 HIS 0.015 0.001 HIS H 310 PHE 0.021 0.001 PHE J 405 TYR 0.012 0.001 TYR G 373 ARG 0.002 0.000 ARG I 255 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 677) hydrogen bonds : angle 4.39386 ( 2046) SS BOND : bond 0.00483 ( 24) SS BOND : angle 0.73815 ( 48) covalent geometry : bond 0.00296 (21824) covalent geometry : angle 0.54558 (29705) *********************** 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 266 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 215 time to evaluate : 2.256 Fit side-chains revert: symmetry clash REVERT: C 277 TRP cc_start: 0.2783 (m100) cc_final: 0.2074 (m-90) REVERT: G 285 HIS cc_start: 0.5651 (m170) cc_final: 0.5274 (m170) REVERT: H 315 ASN cc_start: 0.5903 (m110) cc_final: 0.5360 (p0) REVERT: I 319 TYR cc_start: 0.3214 (m-80) cc_final: 0.2816 (m-80) REVERT: K 358 MET cc_start: 0.3929 (ptp) cc_final: 0.3705 (ptm) REVERT: K 382 GLU cc_start: 0.5067 (mm-30) cc_final: 0.4080 (mm-30) REVERT: K 430 GLU cc_start: 0.6763 (tm-30) cc_final: 0.6352 (tm-30) REVERT: L 358 MET cc_start: 0.2123 (pmm) cc_final: 0.1597 (pmm) outliers start: 51 outliers final: 36 residues processed: 249 average time/residue: 0.2961 time to fit residues: 117.9424 Evaluate side-chains 232 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 2.552 ------------------------------------------------------------------------------- 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 369 VAL Chi-restraints excluded: chain C residue 252 MET 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 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 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 398 LEU Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain H residue 310 HIS 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 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 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 L residue 449 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 129 optimal weight: 7.9990 chunk 10 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 261 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 63 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 ASN F 434 ASN H 310 HIS H 434 ASN I 310 HIS I 325 ASN I 361 ASN ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.210938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.188330 restraints weight = 38898.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.185031 restraints weight = 65034.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.183583 restraints weight = 57955.712| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21848 Z= 0.142 Angle : 0.568 9.584 29753 Z= 0.288 Chirality : 0.044 0.163 3268 Planarity : 0.004 0.044 3821 Dihedral : 3.996 18.601 2848 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.83 % Allowed : 12.68 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.16), residues: 2644 helix: 0.51 (0.37), residues: 213 sheet: 1.76 (0.15), residues: 990 loop : 1.16 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 277 HIS 0.026 0.001 HIS H 310 PHE 0.020 0.002 PHE J 405 TYR 0.014 0.001 TYR H 373 ARG 0.003 0.000 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 677) hydrogen bonds : angle 4.48191 ( 2046) SS BOND : bond 0.00515 ( 24) SS BOND : angle 0.78076 ( 48) covalent geometry : bond 0.00339 (21824) covalent geometry : angle 0.56726 (29705) *********************** 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 281 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 211 time to evaluate : 2.398 Fit side-chains revert: symmetry clash REVERT: A 285 HIS cc_start: 0.4281 (p90) cc_final: 0.3949 (p-80) REVERT: B 347 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6989 (mp10) REVERT: C 277 TRP cc_start: 0.2873 (m100) cc_final: 0.2132 (m-90) REVERT: G 285 HIS cc_start: 0.5705 (m170) cc_final: 0.5470 (m90) REVERT: I 319 TYR cc_start: 0.3253 (m-80) cc_final: 0.2915 (m-80) REVERT: K 382 GLU cc_start: 0.5026 (mm-30) cc_final: 0.4055 (mm-30) REVERT: L 358 MET cc_start: 0.2157 (pmm) cc_final: 0.1766 (pmm) REVERT: L 398 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6340 (tp) outliers start: 70 outliers final: 54 residues processed: 263 average time/residue: 0.2714 time to fit residues: 118.1811 Evaluate side-chains 249 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 2.476 ------------------------------------------------------------------------------- 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 C residue 252 MET 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 376 ASP Chi-restraints excluded: chain C residue 408 SER 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 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 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 369 VAL 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 302 VAL 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 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 307 THR 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 L residue 366 THR Chi-restraints excluded: chain L residue 377 ILE 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 108 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 159 optimal weight: 30.0000 chunk 68 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 198 optimal weight: 30.0000 chunk 238 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN F 434 ASN H 310 HIS I 310 HIS I 361 ASN J 386 GLN ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.207881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.183921 restraints weight = 38634.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.181661 restraints weight = 71240.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.180399 restraints weight = 64075.485| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 21848 Z= 0.218 Angle : 0.672 9.244 29753 Z= 0.347 Chirality : 0.047 0.172 3268 Planarity : 0.004 0.051 3821 Dihedral : 4.628 19.919 2848 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.99 % Allowed : 13.69 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.16), residues: 2644 helix: -0.17 (0.35), residues: 221 sheet: 1.44 (0.15), residues: 985 loop : 0.80 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 417 HIS 0.025 0.002 HIS H 310 PHE 0.021 0.002 PHE G 405 TYR 0.021 0.002 TYR H 373 ARG 0.004 0.001 ARG F 344 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 677) hydrogen bonds : angle 4.93773 ( 2046) SS BOND : bond 0.00699 ( 24) SS BOND : angle 1.05610 ( 48) covalent geometry : bond 0.00519 (21824) covalent geometry : angle 0.67081 (29705) *********************** 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 298 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 224 time to evaluate : 2.255 Fit side-chains revert: symmetry clash REVERT: A 285 HIS cc_start: 0.4528 (p90) cc_final: 0.4058 (p-80) REVERT: A 390 ASN cc_start: 0.4864 (p0) cc_final: 0.3996 (t0) REVERT: B 347 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.7078 (mp10) REVERT: F 312 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.6231 (p0) REVERT: H 442 ASP cc_start: 0.6283 (OUTLIER) cc_final: 0.6066 (m-30) REVERT: J 373 TYR cc_start: 0.5357 (OUTLIER) cc_final: 0.5156 (m-80) REVERT: L 363 VAL cc_start: 0.5665 (t) cc_final: 0.5458 (p) REVERT: L 398 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6416 (tp) REVERT: L 449 THR cc_start: 0.2206 (OUTLIER) cc_final: 0.1869 (t) outliers start: 74 outliers final: 52 residues processed: 280 average time/residue: 0.2839 time to fit residues: 128.6321 Evaluate side-chains 264 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 206 time to evaluate : 2.618 ------------------------------------------------------------------------------- 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 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 B residue 435 HIS Chi-restraints excluded: chain C residue 252 MET 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 376 ASP 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 398 LEU Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 424 SER 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 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 394 THR Chi-restraints excluded: chain G residue 413 ASP Chi-restraints excluded: chain G residue 430 GLU Chi-restraints excluded: chain H residue 252 MET 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 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 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 377 ILE Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 449 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 52 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 20 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 238 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 260 optimal weight: 20.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 434 ASN ** G 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 ASN ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 435 HIS ** L 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.209395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.186796 restraints weight = 38375.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.183319 restraints weight = 59526.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.181854 restraints weight = 52296.853| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21848 Z= 0.132 Angle : 0.588 9.993 29753 Z= 0.298 Chirality : 0.045 0.190 3268 Planarity : 0.004 0.050 3821 Dihedral : 4.316 17.924 2848 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.91 % Allowed : 14.94 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.16), residues: 2644 helix: 0.07 (0.36), residues: 219 sheet: 1.46 (0.15), residues: 970 loop : 0.91 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 417 HIS 0.009 0.001 HIS H 310 PHE 0.020 0.002 PHE J 405 TYR 0.016 0.001 TYR G 373 ARG 0.003 0.000 ARG I 255 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 677) hydrogen bonds : angle 4.68130 ( 2046) SS BOND : bond 0.00511 ( 24) SS BOND : angle 0.80594 ( 48) covalent geometry : bond 0.00315 (21824) covalent geometry : angle 0.58746 (29705) *********************** 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 288 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 216 time to evaluate : 2.378 Fit side-chains revert: symmetry clash REVERT: A 285 HIS cc_start: 0.4476 (p90) cc_final: 0.4002 (p-80) REVERT: A 358 MET cc_start: 0.7616 (mpp) cc_final: 0.7333 (mpp) REVERT: A 390 ASN cc_start: 0.4774 (p0) cc_final: 0.3939 (t0) REVERT: A 457 MET cc_start: -0.0808 (mmm) cc_final: -0.1202 (mmm) REVERT: F 312 ASP cc_start: 0.6755 (OUTLIER) cc_final: 0.6235 (p0) REVERT: F 457 MET cc_start: 0.3094 (mmt) cc_final: 0.2368 (mpp) REVERT: G 437 THR cc_start: 0.8549 (m) cc_final: 0.8318 (m) REVERT: H 442 ASP cc_start: 0.6279 (OUTLIER) cc_final: 0.6010 (p0) REVERT: L 398 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6415 (tp) REVERT: L 449 THR cc_start: 0.2064 (OUTLIER) cc_final: 0.1734 (t) outliers start: 72 outliers final: 57 residues processed: 267 average time/residue: 0.2877 time to fit residues: 124.7741 Evaluate side-chains 269 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 422 VAL 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 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 376 ASP 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 C residue 456 ILE 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 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 426 SER Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 359 THR 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 252 MET 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 307 THR 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 411 THR 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 L residue 377 ILE 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 201 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 251 optimal weight: 0.0040 chunk 113 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 153 optimal weight: 0.0070 chunk 130 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 overall best weight: 4.0016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 310 HIS ** I 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 ASN ** K 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.208409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.186972 restraints weight = 38607.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.183263 restraints weight = 59471.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.181287 restraints weight = 56813.567| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21848 Z= 0.158 Angle : 0.621 11.750 29753 Z= 0.316 Chirality : 0.045 0.174 3268 Planarity : 0.004 0.050 3821 Dihedral : 4.471 22.172 2848 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.19 % Allowed : 15.19 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 2644 helix: -0.01 (0.36), residues: 219 sheet: 1.42 (0.15), residues: 964 loop : 0.84 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 313 HIS 0.007 0.001 HIS H 310 PHE 0.020 0.002 PHE J 405 TYR 0.016 0.001 TYR G 373 ARG 0.009 0.000 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 677) hydrogen bonds : angle 4.76675 ( 2046) SS BOND : bond 0.00561 ( 24) SS BOND : angle 0.88457 ( 48) covalent geometry : bond 0.00378 (21824) covalent geometry : angle 0.62017 (29705) *********************** 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 287 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 208 time to evaluate : 2.659 Fit side-chains REVERT: A 285 HIS cc_start: 0.4630 (p90) cc_final: 0.4098 (p-80) REVERT: A 358 MET cc_start: 0.7575 (mpp) cc_final: 0.7347 (mpp) REVERT: A 390 ASN cc_start: 0.4815 (p0) cc_final: 0.4163 (t0) REVERT: A 391 TYR cc_start: 0.5897 (t80) cc_final: 0.5611 (t80) REVERT: A 457 MET cc_start: -0.0770 (mmm) cc_final: -0.1148 (mmm) REVERT: B 347 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6893 (mp10) REVERT: F 312 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6258 (p0) REVERT: F 449 THR cc_start: 0.2307 (OUTLIER) cc_final: 0.1937 (m) REVERT: F 457 MET cc_start: 0.3082 (mmt) cc_final: 0.2376 (mpp) REVERT: G 437 THR cc_start: 0.8547 (m) cc_final: 0.8310 (m) REVERT: H 442 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.6003 (p0) REVERT: L 449 THR cc_start: 0.2383 (OUTLIER) cc_final: 0.2020 (t) outliers start: 79 outliers final: 65 residues processed: 264 average time/residue: 0.2849 time to fit residues: 122.8893 Evaluate side-chains 270 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 200 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 VAL 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 253 ILE 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 376 ASP 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 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 312 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 VAL 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 426 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 359 THR 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 252 MET 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 442 ASP Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 377 ILE 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 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 377 ILE Chi-restraints excluded: chain L residue 449 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.0857 > 50: distance: 36 - 126: 35.104 distance: 39 - 123: 24.800 distance: 51 - 111: 35.511 distance: 54 - 108: 26.600 distance: 67 - 98: 28.903 distance: 83 - 87: 25.173 distance: 87 - 88: 43.546 distance: 87 - 251: 21.915 distance: 89 - 90: 11.447 distance: 89 - 95: 36.912 distance: 90 - 248: 28.222 distance: 91 - 92: 48.966 distance: 92 - 93: 29.324 distance: 92 - 94: 10.616 distance: 95 - 96: 20.643 distance: 96 - 97: 17.246 distance: 96 - 99: 36.676 distance: 97 - 98: 35.261 distance: 97 - 102: 7.367 distance: 99 - 100: 33.313 distance: 99 - 101: 33.691 distance: 102 - 103: 17.633 distance: 102 - 238: 31.967 distance: 103 - 104: 9.490 distance: 103 - 106: 22.574 distance: 104 - 105: 21.985 distance: 104 - 108: 40.828 distance: 105 - 235: 32.937 distance: 106 - 107: 19.843 distance: 107 - 270: 24.144 distance: 108 - 109: 34.752 distance: 109 - 110: 10.073 distance: 109 - 112: 37.713 distance: 110 - 111: 15.283 distance: 110 - 116: 34.772 distance: 112 - 113: 39.852 distance: 113 - 114: 46.416 distance: 113 - 115: 9.476 distance: 116 - 117: 35.635 distance: 116 - 218: 28.591 distance: 117 - 118: 57.291 distance: 117 - 120: 25.553 distance: 118 - 119: 56.381 distance: 118 - 123: 32.513 distance: 119 - 215: 27.292 distance: 120 - 121: 46.034 distance: 120 - 122: 37.227 distance: 123 - 124: 8.008 distance: 124 - 125: 26.573 distance: 124 - 127: 20.138 distance: 125 - 126: 18.282 distance: 125 - 132: 17.219 distance: 127 - 128: 22.166 distance: 128 - 129: 4.294 distance: 129 - 130: 7.029 distance: 130 - 131: 11.988 distance: 132 - 133: 38.370 distance: 133 - 134: 17.479 distance: 134 - 135: 27.947 distance: 134 - 136: 40.466 distance: 136 - 137: 16.967 distance: 137 - 138: 23.879 distance: 137 - 140: 19.245 distance: 138 - 139: 45.422 distance: 138 - 147: 40.036 distance: 141 - 142: 44.101 distance: 141 - 143: 38.783 distance: 143 - 145: 16.434 distance: 144 - 146: 5.982 distance: 145 - 146: 26.569 distance: 147 - 148: 7.368 distance: 148 - 149: 57.446 distance: 149 - 159: 10.312 distance: 151 - 152: 39.666 distance: 152 - 153: 32.206 distance: 153 - 155: 62.773 distance: 154 - 156: 40.051 distance: 155 - 157: 4.813 distance: 156 - 157: 33.694 distance: 159 - 160: 28.229 distance: 159 - 165: 25.573 distance: 160 - 161: 9.030 distance: 161 - 162: 40.406 distance: 161 - 166: 30.508