Starting phenix.real_space_refine on Thu Feb 5 21:48:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uo4_64372/02_2026/9uo4_64372.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uo4_64372/02_2026/9uo4_64372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uo4_64372/02_2026/9uo4_64372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uo4_64372/02_2026/9uo4_64372.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uo4_64372/02_2026/9uo4_64372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uo4_64372/02_2026/9uo4_64372.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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 84 5.16 5 C 12576 2.51 5 N 3420 2.21 5 O 3900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19980 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain: "B" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain: "C" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain: "D" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain: "E" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain: "F" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain: "G" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain: "H" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain: "I" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain: "J" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain: "K" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Chain: "L" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1665 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 17, 'TRANS': 196} Time building chain proxies: 3.89, per 1000 atoms: 0.19 Number of scatterers: 19980 At special positions: 0 Unit cell: (59.92, 175.48, 186.18, 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 84 16.00 O 3900 8.00 N 3420 7.00 C 12576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.03 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.03 Simple disulfide: pdb=" SG CYS I 367 " - pdb=" SG CYS I 426 " distance=2.03 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 536 " distance=2.04 Simple disulfide: pdb=" SG CYS J 367 " - pdb=" SG CYS J 426 " distance=2.03 Simple disulfide: pdb=" SG CYS J 474 " - pdb=" SG CYS J 536 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 634.5 milliseconds 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 50 sheets defined 13.2% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 460 through 467 Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.532A pdb=" N THR A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 460 through 467 removed outlier: 4.094A pdb=" N LEU B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 530 removed outlier: 3.639A pdb=" N TRP B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 460 through 465 removed outlier: 3.826A pdb=" N LEU C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 529 removed outlier: 3.645A pdb=" N TRP C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 460 through 466 Processing helix chain 'D' and resid 525 through 530 Processing helix chain 'E' and resid 353 through 360 removed outlier: 3.799A pdb=" N ILE E 357 " --> pdb=" O SER E 353 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE E 358 " --> pdb=" O PHE E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 420 Processing helix chain 'E' and resid 462 through 467 Processing helix chain 'E' and resid 524 through 529 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 460 through 467 removed outlier: 3.759A pdb=" N LEU F 464 " --> pdb=" O ALA F 460 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU F 466 " --> pdb=" O GLU F 462 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG F 467 " --> pdb=" O GLN F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 529 Processing helix chain 'G' and resid 353 through 358 Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 460 through 467 removed outlier: 3.870A pdb=" N LEU G 464 " --> pdb=" O ALA G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 530 Processing helix chain 'H' and resid 353 through 360 Processing helix chain 'H' and resid 414 through 420 Processing helix chain 'H' and resid 460 through 465 Processing helix chain 'H' and resid 525 through 529 Processing helix chain 'I' and resid 353 through 361 removed outlier: 4.009A pdb=" N THR I 360 " --> pdb=" O SER I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 419 Processing helix chain 'I' and resid 460 through 467 removed outlier: 4.231A pdb=" N LEU I 464 " --> pdb=" O ALA I 460 " (cutoff:3.500A) Processing helix chain 'I' and resid 524 through 530 removed outlier: 3.556A pdb=" N TRP I 528 " --> pdb=" O SER I 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 353 through 361 removed outlier: 4.103A pdb=" N THR J 360 " --> pdb=" O SER J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 421 removed outlier: 3.657A pdb=" N GLY J 421 " --> pdb=" O ASP J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 466 removed outlier: 4.087A pdb=" N LEU J 466 " --> pdb=" O GLU J 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 524 through 530 Processing helix chain 'K' and resid 355 through 360 removed outlier: 3.529A pdb=" N THR K 360 " --> pdb=" O SER K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 419 Processing helix chain 'K' and resid 460 through 465 removed outlier: 3.801A pdb=" N LEU K 464 " --> pdb=" O ALA K 460 " (cutoff:3.500A) Processing helix chain 'K' and resid 524 through 530 removed outlier: 3.640A pdb=" N THR K 530 " --> pdb=" O GLU K 526 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 360 removed outlier: 3.632A pdb=" N THR L 360 " --> pdb=" O SER L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 419 Processing helix chain 'L' and resid 460 through 467 Processing helix chain 'L' and resid 524 through 530 removed outlier: 3.559A pdb=" N TRP L 528 " --> pdb=" O SER L 524 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 455 through 457 removed outlier: 3.511A pdb=" N THR A 473 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.637A pdb=" N VAL A 501 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 490 removed outlier: 3.855A pdb=" N THR A 535 " --> pdb=" O MET A 489 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 550 " --> pdb=" O CYS A 536 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 363 through 365 removed outlier: 3.935A pdb=" N THR B 363 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 413 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 365 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 411 " --> pdb=" O LEU B 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.669A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 519 " --> pdb=" O CYS B 474 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS B 518 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 501 " --> pdb=" O ILE B 520 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 470 through 471 removed outlier: 4.217A pdb=" N VAL B 523 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.618A pdb=" N GLN B 487 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 535 " --> pdb=" O MET B 489 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 453 through 457 Processing sheet with id=AA9, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.898A pdb=" N VAL C 523 " --> pdb=" O ALA C 470 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 493 through 495 removed outlier: 4.478A pdb=" N TRP C 488 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR C 534 " --> pdb=" O VAL C 552 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 552 " --> pdb=" O TYR C 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 502 through 503 removed outlier: 3.847A pdb=" N HIS C 518 " --> pdb=" O SER C 503 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 380 through 381 removed outlier: 4.181A pdb=" N SER D 381 " --> pdb=" O THR D 427 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 424 through 425 removed outlier: 4.292A pdb=" N PHE D 424 " --> pdb=" O ILE D 441 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 453 through 457 removed outlier: 3.505A pdb=" N SER D 519 " --> pdb=" O CYS D 474 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 501 " --> pdb=" O ILE D 520 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 485 through 489 removed outlier: 3.679A pdb=" N THR D 548 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 485 through 489 removed outlier: 3.525A pdb=" N TYR D 534 " --> pdb=" O VAL D 552 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 506 through 507 Processing sheet with id=AB9, first strand: chain 'E' and resid 347 through 350 removed outlier: 3.685A pdb=" N ILE E 350 " --> pdb=" O THR E 366 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 363 through 364 removed outlier: 4.717A pdb=" N THR E 363 " --> pdb=" O ILE E 413 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.618A pdb=" N ILE E 472 " --> pdb=" O LEU E 521 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER E 519 " --> pdb=" O CYS E 474 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 501 " --> pdb=" O ILE E 520 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 453 through 457 removed outlier: 5.107A pdb=" N THR E 477 " --> pdb=" O ALA E 517 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA E 517 " --> pdb=" O THR E 477 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET E 506 " --> pdb=" O PHE E 516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 486 through 490 removed outlier: 3.669A pdb=" N THR E 535 " --> pdb=" O MET E 489 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 455 through 457 removed outlier: 3.682A pdb=" N THR F 473 " --> pdb=" O LEU F 457 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA F 517 " --> pdb=" O VAL F 476 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 501 " --> pdb=" O ILE F 520 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 455 through 457 removed outlier: 3.682A pdb=" N THR F 473 " --> pdb=" O LEU F 457 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA F 517 " --> pdb=" O VAL F 476 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 493 through 494 removed outlier: 3.818A pdb=" N GLN F 490 " --> pdb=" O GLN F 493 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR F 534 " --> pdb=" O VAL F 552 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG F 550 " --> pdb=" O CYS F 536 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 348 through 350 removed outlier: 3.554A pdb=" N LEU G 368 " --> pdb=" O PHE G 348 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE G 350 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 363 through 364 removed outlier: 4.718A pdb=" N THR G 363 " --> pdb=" O ILE G 413 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 470 through 473 removed outlier: 3.590A pdb=" N VAL G 523 " --> pdb=" O ALA G 470 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA G 517 " --> pdb=" O THR G 477 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR G 477 " --> pdb=" O ALA G 517 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 470 through 473 removed outlier: 3.590A pdb=" N VAL G 523 " --> pdb=" O ALA G 470 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N HIS G 518 " --> pdb=" O ALA G 504 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA G 504 " --> pdb=" O HIS G 518 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE G 520 " --> pdb=" O THR G 502 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N THR G 502 " --> pdb=" O ILE G 520 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 485 through 489 removed outlier: 3.553A pdb=" N THR G 535 " --> pdb=" O MET G 489 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR G 548 " --> pdb=" O VAL G 538 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 363 through 365 removed outlier: 4.723A pdb=" N THR H 363 " --> pdb=" O ILE H 413 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE H 413 " --> pdb=" O THR H 363 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 453 through 457 Processing sheet with id=AD6, first strand: chain 'H' and resid 469 through 471 Processing sheet with id=AD7, first strand: chain 'H' and resid 485 through 489 removed outlier: 3.719A pdb=" N THR H 535 " --> pdb=" O MET H 489 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR H 548 " --> pdb=" O VAL H 538 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 381 through 383 removed outlier: 4.249A pdb=" N SER I 381 " --> pdb=" O THR I 427 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR I 427 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR I 383 " --> pdb=" O THR I 425 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 425 " --> pdb=" O THR I 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 455 through 457 removed outlier: 5.425A pdb=" N TYR I 515 " --> pdb=" O GLY I 478 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 470 through 471 Processing sheet with id=AE2, first strand: chain 'I' and resid 493 through 494 removed outlier: 3.700A pdb=" N THR I 535 " --> pdb=" O MET I 489 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG I 550 " --> pdb=" O CYS I 536 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR I 548 " --> pdb=" O VAL I 538 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 454 through 457 removed outlier: 3.525A pdb=" N THR J 473 " --> pdb=" O LEU J 457 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER J 519 " --> pdb=" O CYS J 474 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL J 476 " --> pdb=" O ALA J 517 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 454 through 457 removed outlier: 3.525A pdb=" N THR J 473 " --> pdb=" O LEU J 457 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER J 519 " --> pdb=" O CYS J 474 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL J 476 " --> pdb=" O ALA J 517 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 493 through 494 removed outlier: 3.511A pdb=" N THR J 548 " --> pdb=" O VAL J 538 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 454 through 457 removed outlier: 3.908A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL K 523 " --> pdb=" O ALA K 470 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER K 519 " --> pdb=" O CYS K 474 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL K 501 " --> pdb=" O ILE K 520 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 454 through 457 removed outlier: 3.908A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY K 478 " --> pdb=" O TYR K 515 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET K 506 " --> pdb=" O PHE K 516 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 493 through 494 Processing sheet with id=AE9, first strand: chain 'L' and resid 363 through 365 removed outlier: 4.343A pdb=" N THR L 363 " --> pdb=" O ILE L 413 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU L 365 " --> pdb=" O ALA L 411 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA L 411 " --> pdb=" O LEU L 365 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 378 through 381 removed outlier: 4.133A pdb=" N THR L 379 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR L 429 " --> pdb=" O THR L 379 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 455 through 457 removed outlier: 4.071A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 472 " --> pdb=" O LEU L 521 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER L 519 " --> pdb=" O CYS L 474 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 455 through 457 removed outlier: 4.071A pdb=" N THR L 473 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N THR L 477 " --> pdb=" O ALA L 517 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA L 517 " --> pdb=" O THR L 477 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 485 through 489 removed outlier: 3.958A pdb=" N THR L 535 " --> pdb=" O MET L 489 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 485 through 489 removed outlier: 3.958A pdb=" N THR L 535 " --> pdb=" O MET L 489 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6542 1.34 - 1.46: 4622 1.46 - 1.58: 9224 1.58 - 1.70: 0 1.70 - 1.83: 108 Bond restraints: 20496 Sorted by residual: bond pdb=" CA SER J 406 " pdb=" CB SER J 406 " ideal model delta sigma weight residual 1.527 1.551 -0.024 1.75e-02 3.27e+03 1.90e+00 bond pdb=" N VAL B 523 " pdb=" CA VAL B 523 " ideal model delta sigma weight residual 1.459 1.445 0.014 1.25e-02 6.40e+03 1.33e+00 bond pdb=" CE2 PHE B 516 " pdb=" CZ PHE B 516 " ideal model delta sigma weight residual 1.382 1.348 0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" CA SER G 480 " pdb=" C SER G 480 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.26e-02 6.30e+03 1.25e+00 bond pdb=" CA CYS F 367 " pdb=" CB CYS F 367 " ideal model delta sigma weight residual 1.531 1.566 -0.036 3.28e-02 9.30e+02 1.19e+00 ... (remaining 20491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 27457 2.16 - 4.31: 520 4.31 - 6.47: 66 6.47 - 8.63: 9 8.63 - 10.78: 4 Bond angle restraints: 28056 Sorted by residual: angle pdb=" C SER B 420 " pdb=" CA SER B 420 " pdb=" CB SER B 420 " ideal model delta sigma weight residual 116.54 112.59 3.95 1.15e+00 7.56e-01 1.18e+01 angle pdb=" C ASN K 545 " pdb=" N ARG K 546 " pdb=" CA ARG K 546 " ideal model delta sigma weight residual 121.54 127.93 -6.39 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C ASN D 545 " pdb=" N ARG D 546 " pdb=" CA ARG D 546 " ideal model delta sigma weight residual 121.54 127.29 -5.75 1.91e+00 2.74e-01 9.07e+00 angle pdb=" C ASN I 545 " pdb=" N ARG I 546 " pdb=" CA ARG I 546 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.14e+00 angle pdb=" C ASN L 545 " pdb=" N ARG L 546 " pdb=" CA ARG L 546 " ideal model delta sigma weight residual 121.54 126.89 -5.35 1.91e+00 2.74e-01 7.83e+00 ... (remaining 28051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 11209 17.79 - 35.58: 981 35.58 - 53.38: 175 53.38 - 71.17: 40 71.17 - 88.96: 27 Dihedral angle restraints: 12432 sinusoidal: 4896 harmonic: 7536 Sorted by residual: dihedral pdb=" CB CYS J 367 " pdb=" SG CYS J 367 " pdb=" SG CYS J 426 " pdb=" CB CYS J 426 " ideal model delta sinusoidal sigma weight residual 93.00 33.16 59.84 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS D 367 " pdb=" SG CYS D 367 " pdb=" SG CYS D 426 " pdb=" CB CYS D 426 " ideal model delta sinusoidal sigma weight residual 93.00 33.25 59.75 1 1.00e+01 1.00e-02 4.76e+01 dihedral pdb=" CB CYS I 367 " pdb=" SG CYS I 367 " pdb=" SG CYS I 426 " pdb=" CB CYS I 426 " ideal model delta sinusoidal sigma weight residual 93.00 33.92 59.08 1 1.00e+01 1.00e-02 4.67e+01 ... (remaining 12429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2311 0.046 - 0.092: 742 0.092 - 0.138: 195 0.138 - 0.184: 19 0.184 - 0.230: 9 Chirality restraints: 3276 Sorted by residual: chirality pdb=" CB THR F 522 " pdb=" CA THR F 522 " pdb=" OG1 THR F 522 " pdb=" CG2 THR F 522 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB THR F 471 " pdb=" CA THR F 471 " pdb=" OG1 THR F 471 " pdb=" CG2 THR F 471 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB THR G 522 " pdb=" CA THR G 522 " pdb=" OG1 THR G 522 " pdb=" CG2 THR G 522 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3273 not shown) Planarity restraints: 3612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG I 443 " 0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO I 444 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO I 444 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 444 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 400 " -0.044 5.00e-02 4.00e+02 6.74e-02 7.28e+00 pdb=" N PRO G 401 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO G 401 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 401 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 504 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO C 505 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 505 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 505 " 0.035 5.00e-02 4.00e+02 ... (remaining 3609 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 10946 3.02 - 3.49: 21015 3.49 - 3.96: 33157 3.96 - 4.43: 38046 4.43 - 4.90: 59668 Nonbonded interactions: 162832 Sorted by model distance: nonbonded pdb=" N GLU J 468 " pdb=" O GLU J 468 " model vdw 2.552 2.496 nonbonded pdb=" N ASP H 553 " pdb=" O ASP H 553 " model vdw 2.602 2.496 nonbonded pdb=" O SER L 406 " pdb=" OG SER L 406 " model vdw 2.608 3.040 nonbonded pdb=" N PHE C 516 " pdb=" O PHE C 516 " model vdw 2.618 2.496 nonbonded pdb=" O SER E 406 " pdb=" OG SER E 406 " model vdw 2.619 3.040 ... (remaining 162827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.180 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20520 Z= 0.142 Angle : 0.701 10.782 28104 Z= 0.360 Chirality : 0.048 0.230 3276 Planarity : 0.006 0.073 3612 Dihedral : 14.301 88.961 7440 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.15), residues: 2544 helix: -2.51 (0.22), residues: 345 sheet: -3.19 (0.16), residues: 743 loop : -1.71 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 491 TYR 0.014 0.002 TYR H 455 PHE 0.023 0.002 PHE A 358 TRP 0.015 0.002 TRP L 488 HIS 0.010 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00307 (20496) covalent geometry : angle 0.70033 (28056) SS BOND : bond 0.00243 ( 24) SS BOND : angle 0.98268 ( 48) hydrogen bonds : bond 0.23739 ( 390) hydrogen bonds : angle 12.06540 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 LYS cc_start: 0.6345 (mmtt) cc_final: 0.5721 (tppt) REVERT: E 382 TRP cc_start: 0.1004 (m100) cc_final: -0.1644 (m100) REVERT: E 528 TRP cc_start: 0.5445 (t60) cc_final: 0.5139 (t-100) REVERT: F 546 ARG cc_start: 0.6994 (tpp-160) cc_final: 0.5803 (ttp-110) REVERT: J 462 GLU cc_start: 0.5603 (mt-10) cc_final: 0.4839 (tm-30) REVERT: K 471 THR cc_start: 0.4871 (m) cc_final: 0.4369 (p) REVERT: L 483 ASP cc_start: 0.7473 (t70) cc_final: 0.7225 (t70) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.1525 time to fit residues: 97.8631 Evaluate side-chains 279 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 30.0000 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 HIS ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 HIS ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 ASN H 419 ASN I 490 GLN ** J 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS L 450 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.281052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.238514 restraints weight = 22047.815| |-----------------------------------------------------------------------------| r_work (start): 0.4683 rms_B_bonded: 3.30 r_work: 0.4274 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 20520 Z= 0.223 Angle : 0.685 10.945 28104 Z= 0.348 Chirality : 0.047 0.190 3276 Planarity : 0.006 0.056 3612 Dihedral : 5.406 23.855 2748 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.32 % Allowed : 9.61 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.16), residues: 2544 helix: -2.13 (0.24), residues: 321 sheet: -3.11 (0.18), residues: 615 loop : -1.51 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 443 TYR 0.019 0.002 TYR E 534 PHE 0.024 0.002 PHE E 479 TRP 0.030 0.002 TRP A 528 HIS 0.009 0.002 HIS E 540 Details of bonding type rmsd covalent geometry : bond 0.00535 (20496) covalent geometry : angle 0.68420 (28056) SS BOND : bond 0.00712 ( 24) SS BOND : angle 0.96945 ( 48) hydrogen bonds : bond 0.04366 ( 390) hydrogen bonds : angle 8.74686 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 309 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 488 TRP cc_start: 0.7398 (m100) cc_final: 0.7159 (m100) REVERT: C 418 TRP cc_start: 0.6093 (t-100) cc_final: 0.5501 (t60) REVERT: D 538 VAL cc_start: 0.8642 (t) cc_final: 0.8346 (t) REVERT: E 382 TRP cc_start: 0.0928 (m100) cc_final: -0.1407 (m100) REVERT: F 546 ARG cc_start: 0.7286 (tpp-160) cc_final: 0.5723 (ttp-110) REVERT: G 358 PHE cc_start: 0.5461 (m-10) cc_final: 0.4962 (m-80) REVERT: G 443 ARG cc_start: 0.7242 (mmm-85) cc_final: 0.6963 (mtp180) REVERT: G 456 LEU cc_start: 0.8729 (tp) cc_final: 0.8396 (tp) REVERT: J 462 GLU cc_start: 0.6063 (mt-10) cc_final: 0.4920 (tm-30) REVERT: K 471 THR cc_start: 0.5846 (m) cc_final: 0.5074 (p) REVERT: L 483 ASP cc_start: 0.7670 (t70) cc_final: 0.7341 (t70) outliers start: 30 outliers final: 23 residues processed: 327 average time/residue: 0.1404 time to fit residues: 69.6488 Evaluate side-chains 281 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 395 ASN Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 527 GLU Chi-restraints excluded: chain J residue 533 THR Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain L residue 393 HIS Chi-restraints excluded: chain L residue 462 GLU Chi-restraints excluded: chain L residue 473 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 135 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 176 optimal weight: 30.0000 chunk 196 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 111 optimal weight: 40.0000 chunk 188 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 184 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN B 487 GLN D 393 HIS E 490 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 ASN ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN K 529 ASN L 393 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.280546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.237418 restraints weight = 22085.430| |-----------------------------------------------------------------------------| r_work (start): 0.4690 rms_B_bonded: 3.22 r_work: 0.4286 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20520 Z= 0.173 Angle : 0.632 9.404 28104 Z= 0.318 Chirality : 0.046 0.209 3276 Planarity : 0.005 0.049 3612 Dihedral : 5.181 23.067 2748 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 1.80 % Allowed : 12.24 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.16), residues: 2544 helix: -1.98 (0.23), residues: 360 sheet: -3.02 (0.18), residues: 619 loop : -1.51 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 451 TYR 0.014 0.001 TYR F 375 PHE 0.030 0.002 PHE C 485 TRP 0.020 0.002 TRP I 418 HIS 0.009 0.001 HIS L 393 Details of bonding type rmsd covalent geometry : bond 0.00416 (20496) covalent geometry : angle 0.63176 (28056) SS BOND : bond 0.00460 ( 24) SS BOND : angle 0.79828 ( 48) hydrogen bonds : bond 0.03728 ( 390) hydrogen bonds : angle 8.15784 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 532 GLU cc_start: 0.7083 (pt0) cc_final: 0.6830 (tm-30) REVERT: E 382 TRP cc_start: 0.0877 (m100) cc_final: -0.1586 (m100) REVERT: F 451 ARG cc_start: 0.7179 (ptm-80) cc_final: 0.6839 (ptm-80) REVERT: F 546 ARG cc_start: 0.7314 (tpp-160) cc_final: 0.5684 (ttp-110) REVERT: F 553 ASP cc_start: 0.5698 (m-30) cc_final: 0.5475 (m-30) REVERT: G 358 PHE cc_start: 0.5523 (m-10) cc_final: 0.5052 (m-80) REVERT: G 418 TRP cc_start: 0.7543 (t-100) cc_final: 0.6908 (t-100) REVERT: G 456 LEU cc_start: 0.8662 (tp) cc_final: 0.8358 (tp) REVERT: H 477 THR cc_start: 0.7250 (OUTLIER) cc_final: 0.6830 (t) REVERT: J 462 GLU cc_start: 0.5766 (mt-10) cc_final: 0.4650 (tm-30) REVERT: L 483 ASP cc_start: 0.7555 (t70) cc_final: 0.7262 (t70) REVERT: L 489 MET cc_start: 0.6790 (mmm) cc_final: 0.6151 (mmm) outliers start: 41 outliers final: 29 residues processed: 294 average time/residue: 0.1444 time to fit residues: 64.8407 Evaluate side-chains 274 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 375 TYR Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain H residue 527 GLU Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 503 SER Chi-restraints excluded: chain L residue 462 GLU Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 473 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 53 optimal weight: 0.5980 chunk 223 optimal weight: 0.6980 chunk 247 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 149 optimal weight: 0.2980 chunk 168 optimal weight: 9.9990 chunk 190 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 HIS ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN K 529 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.277981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.235743 restraints weight = 22023.633| |-----------------------------------------------------------------------------| r_work (start): 0.4681 rms_B_bonded: 3.47 r_work: 0.4233 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 20520 Z= 0.200 Angle : 0.639 9.354 28104 Z= 0.322 Chirality : 0.046 0.237 3276 Planarity : 0.005 0.049 3612 Dihedral : 5.158 22.324 2748 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.54 % Allowed : 13.55 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.16), residues: 2544 helix: -1.79 (0.24), residues: 355 sheet: -3.00 (0.19), residues: 591 loop : -1.40 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 443 TYR 0.023 0.002 TYR A 534 PHE 0.024 0.002 PHE K 479 TRP 0.028 0.002 TRP C 418 HIS 0.007 0.001 HIS D 518 Details of bonding type rmsd covalent geometry : bond 0.00485 (20496) covalent geometry : angle 0.63820 (28056) SS BOND : bond 0.00531 ( 24) SS BOND : angle 0.87598 ( 48) hydrogen bonds : bond 0.03647 ( 390) hydrogen bonds : angle 7.94279 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 274 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 488 TRP cc_start: 0.7483 (m100) cc_final: 0.7226 (m100) REVERT: E 382 TRP cc_start: 0.0856 (m100) cc_final: -0.1624 (m100) REVERT: E 454 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7896 (p) REVERT: F 546 ARG cc_start: 0.7486 (tpp-160) cc_final: 0.5799 (ttp-110) REVERT: F 553 ASP cc_start: 0.5858 (m-30) cc_final: 0.5614 (m-30) REVERT: G 358 PHE cc_start: 0.5515 (m-10) cc_final: 0.5082 (m-80) REVERT: G 418 TRP cc_start: 0.7414 (t-100) cc_final: 0.6807 (t-100) REVERT: G 456 LEU cc_start: 0.8818 (tp) cc_final: 0.8486 (tp) REVERT: H 477 THR cc_start: 0.7309 (OUTLIER) cc_final: 0.6859 (t) REVERT: H 487 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: I 410 GLU cc_start: 0.7369 (mp0) cc_final: 0.6924 (mp0) REVERT: J 462 GLU cc_start: 0.5920 (mt-10) cc_final: 0.4686 (tm-30) REVERT: J 506 MET cc_start: 0.7424 (pmm) cc_final: 0.7004 (pmm) REVERT: L 413 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6868 (mt) REVERT: L 483 ASP cc_start: 0.7646 (t70) cc_final: 0.7397 (t70) REVERT: L 489 MET cc_start: 0.7090 (mmm) cc_final: 0.6186 (mmm) outliers start: 58 outliers final: 43 residues processed: 315 average time/residue: 0.1435 time to fit residues: 68.6921 Evaluate side-chains 285 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain G residue 471 THR Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 487 GLN Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain J residue 533 THR Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 503 SER Chi-restraints excluded: chain L residue 413 ILE Chi-restraints excluded: chain L residue 462 GLU Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 510 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 116 optimal weight: 0.8980 chunk 232 optimal weight: 0.0470 chunk 146 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 226 optimal weight: 0.8980 chunk 230 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 118 optimal weight: 0.2980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 GLN D 393 HIS ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN H 419 ASN H 510 GLN J 490 GLN K 529 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.279571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.241508 restraints weight = 22186.785| |-----------------------------------------------------------------------------| r_work (start): 0.4755 rms_B_bonded: 2.62 r_work: 0.4406 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20520 Z= 0.162 Angle : 0.615 8.852 28104 Z= 0.308 Chirality : 0.045 0.219 3276 Planarity : 0.005 0.046 3612 Dihedral : 5.042 22.558 2748 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.59 % Allowed : 15.53 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.16), residues: 2544 helix: -1.67 (0.25), residues: 355 sheet: -2.96 (0.18), residues: 638 loop : -1.31 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 443 TYR 0.013 0.001 TYR A 534 PHE 0.032 0.002 PHE C 485 TRP 0.031 0.001 TRP C 418 HIS 0.010 0.001 HIS F 518 Details of bonding type rmsd covalent geometry : bond 0.00395 (20496) covalent geometry : angle 0.61419 (28056) SS BOND : bond 0.00398 ( 24) SS BOND : angle 1.12323 ( 48) hydrogen bonds : bond 0.03299 ( 390) hydrogen bonds : angle 7.60370 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 254 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 488 TRP cc_start: 0.7401 (m100) cc_final: 0.7198 (m100) REVERT: E 382 TRP cc_start: 0.0669 (m100) cc_final: -0.1647 (m100) REVERT: E 454 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7756 (p) REVERT: E 534 TYR cc_start: 0.5084 (m-80) cc_final: 0.4796 (m-80) REVERT: F 487 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: F 546 ARG cc_start: 0.7464 (tpp-160) cc_final: 0.5970 (ttp-110) REVERT: F 553 ASP cc_start: 0.5657 (m-30) cc_final: 0.5456 (m-30) REVERT: G 358 PHE cc_start: 0.5481 (m-10) cc_final: 0.5115 (m-80) REVERT: G 418 TRP cc_start: 0.7443 (t-100) cc_final: 0.6980 (t-100) REVERT: G 456 LEU cc_start: 0.8684 (tp) cc_final: 0.8403 (tp) REVERT: G 558 LYS cc_start: 0.4234 (mmtt) cc_final: 0.3720 (mtpt) REVERT: H 477 THR cc_start: 0.7146 (OUTLIER) cc_final: 0.6730 (t) REVERT: I 410 GLU cc_start: 0.7086 (mp0) cc_final: 0.6846 (mp0) REVERT: J 457 LEU cc_start: 0.8887 (mt) cc_final: 0.8294 (mp) REVERT: J 462 GLU cc_start: 0.5695 (mt-10) cc_final: 0.4604 (tm-30) REVERT: J 506 MET cc_start: 0.7070 (pmm) cc_final: 0.6856 (pmm) REVERT: L 483 ASP cc_start: 0.7304 (t70) cc_final: 0.7081 (t70) REVERT: L 489 MET cc_start: 0.6684 (mmm) cc_final: 0.6078 (mmm) outliers start: 59 outliers final: 44 residues processed: 298 average time/residue: 0.1440 time to fit residues: 65.8336 Evaluate side-chains 283 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 471 THR Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 529 ASN Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 503 SER Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 510 GLN Chi-restraints excluded: chain L residue 521 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 73 optimal weight: 0.4980 chunk 42 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 203 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 chunk 242 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 232 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 GLN D 393 HIS ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5022 r_free = 0.5022 target = 0.278549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.237076 restraints weight = 21876.120| |-----------------------------------------------------------------------------| r_work (start): 0.4690 rms_B_bonded: 3.30 r_work: 0.4240 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20520 Z= 0.175 Angle : 0.621 8.695 28104 Z= 0.312 Chirality : 0.045 0.185 3276 Planarity : 0.005 0.048 3612 Dihedral : 4.998 21.327 2748 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.25 % Allowed : 16.32 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.16), residues: 2544 helix: -1.65 (0.25), residues: 353 sheet: -2.94 (0.18), residues: 642 loop : -1.27 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 443 TYR 0.021 0.001 TYR F 375 PHE 0.019 0.002 PHE J 479 TRP 0.020 0.002 TRP I 418 HIS 0.007 0.001 HIS D 518 Details of bonding type rmsd covalent geometry : bond 0.00427 (20496) covalent geometry : angle 0.62030 (28056) SS BOND : bond 0.00447 ( 24) SS BOND : angle 0.93670 ( 48) hydrogen bonds : bond 0.03341 ( 390) hydrogen bonds : angle 7.52451 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 256 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 382 TRP cc_start: 0.0825 (m100) cc_final: -0.1659 (m100) REVERT: E 454 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.7924 (p) REVERT: E 534 TYR cc_start: 0.5258 (m-80) cc_final: 0.4961 (m-80) REVERT: F 487 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: F 518 HIS cc_start: 0.6965 (OUTLIER) cc_final: 0.6755 (t-90) REVERT: F 546 ARG cc_start: 0.7587 (tpp-160) cc_final: 0.6017 (ttp-110) REVERT: F 553 ASP cc_start: 0.5831 (m-30) cc_final: 0.5601 (m-30) REVERT: G 358 PHE cc_start: 0.5570 (m-80) cc_final: 0.5041 (m-80) REVERT: G 418 TRP cc_start: 0.7436 (t-100) cc_final: 0.6959 (t-100) REVERT: G 456 LEU cc_start: 0.8808 (tp) cc_final: 0.8484 (tp) REVERT: G 558 LYS cc_start: 0.4336 (mmtt) cc_final: 0.3783 (mtpt) REVERT: H 477 THR cc_start: 0.7245 (OUTLIER) cc_final: 0.6817 (t) REVERT: H 487 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7606 (pm20) REVERT: I 410 GLU cc_start: 0.7539 (mp0) cc_final: 0.7121 (mp0) REVERT: J 462 GLU cc_start: 0.5626 (mt-10) cc_final: 0.4524 (tm-30) REVERT: L 483 ASP cc_start: 0.7588 (t70) cc_final: 0.7136 (t70) REVERT: L 489 MET cc_start: 0.6818 (mmm) cc_final: 0.6041 (mmm) outliers start: 74 outliers final: 60 residues processed: 313 average time/residue: 0.1357 time to fit residues: 65.8159 Evaluate side-chains 297 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 549 GLU Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 471 THR Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 487 GLN Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 476 VAL Chi-restraints excluded: chain J residue 518 HIS Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 447 VAL Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 503 SER Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain L residue 462 GLU Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 510 GLN Chi-restraints excluded: chain L residue 521 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 246 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 219 optimal weight: 20.0000 chunk 119 optimal weight: 0.6980 chunk 194 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 HIS ** D 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN H 419 ASN ** H 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 529 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.270589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.201207 restraints weight = 21568.912| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 3.38 r_work: 0.4042 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.171 20520 Z= 0.397 Angle : 0.803 12.102 28104 Z= 0.413 Chirality : 0.051 0.285 3276 Planarity : 0.006 0.050 3612 Dihedral : 5.623 26.525 2748 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 4.17 % Allowed : 16.32 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.16), residues: 2544 helix: -1.61 (0.25), residues: 348 sheet: -3.11 (0.20), residues: 531 loop : -1.50 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 550 TYR 0.021 0.003 TYR C 500 PHE 0.034 0.003 PHE C 485 TRP 0.045 0.002 TRP A 418 HIS 0.012 0.002 HIS K 450 Details of bonding type rmsd covalent geometry : bond 0.00943 (20496) covalent geometry : angle 0.80153 (28056) SS BOND : bond 0.01051 ( 24) SS BOND : angle 1.27886 ( 48) hydrogen bonds : bond 0.04577 ( 390) hydrogen bonds : angle 8.73332 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 264 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6297 (tppt) REVERT: B 487 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: B 488 TRP cc_start: 0.7876 (m100) cc_final: 0.6898 (m100) REVERT: B 528 TRP cc_start: 0.5791 (t60) cc_final: 0.5373 (t60) REVERT: B 534 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.5957 (t80) REVERT: D 348 PHE cc_start: 0.3117 (t80) cc_final: 0.2826 (t80) REVERT: E 382 TRP cc_start: 0.1339 (m100) cc_final: -0.1484 (m100) REVERT: E 454 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8250 (p) REVERT: F 487 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: G 558 LYS cc_start: 0.4531 (mmtt) cc_final: 0.3825 (mtpt) REVERT: H 487 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: I 410 GLU cc_start: 0.7789 (mp0) cc_final: 0.7048 (mp0) REVERT: J 546 ARG cc_start: 0.7545 (ttt-90) cc_final: 0.7185 (ttt180) REVERT: L 483 ASP cc_start: 0.7664 (t70) cc_final: 0.7366 (t70) REVERT: L 489 MET cc_start: 0.7344 (mmm) cc_final: 0.6462 (mmm) REVERT: L 527 GLU cc_start: 0.6520 (tt0) cc_final: 0.6239 (tt0) outliers start: 95 outliers final: 74 residues processed: 329 average time/residue: 0.1463 time to fit residues: 72.3045 Evaluate side-chains 314 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 235 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 471 THR Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 523 VAL Chi-restraints excluded: chain G residue 529 ASN Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 487 GLN Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain H residue 548 THR Chi-restraints excluded: chain I residue 417 ASP Chi-restraints excluded: chain I residue 471 THR Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 533 THR Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 447 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 503 SER Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain L residue 462 GLU Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 548 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 220 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 HIS D 419 ASN ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN H 419 ASN H 510 GLN ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 529 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.273311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.209272 restraints weight = 21969.837| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 3.16 r_work: 0.4158 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 20520 Z= 0.214 Angle : 0.690 12.813 28104 Z= 0.346 Chirality : 0.047 0.338 3276 Planarity : 0.005 0.053 3612 Dihedral : 5.399 23.357 2748 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.42 % Allowed : 17.63 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.16), residues: 2544 helix: -1.64 (0.25), residues: 350 sheet: -3.07 (0.20), residues: 512 loop : -1.46 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 451 TYR 0.027 0.002 TYR B 500 PHE 0.026 0.002 PHE C 485 TRP 0.023 0.002 TRP A 418 HIS 0.020 0.002 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00517 (20496) covalent geometry : angle 0.68910 (28056) SS BOND : bond 0.00573 ( 24) SS BOND : angle 1.04811 ( 48) hydrogen bonds : bond 0.03520 ( 390) hydrogen bonds : angle 8.07536 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 248 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 LYS cc_start: 0.6990 (mmtt) cc_final: 0.6247 (tppt) REVERT: B 488 TRP cc_start: 0.7643 (m100) cc_final: 0.6921 (m100) REVERT: B 528 TRP cc_start: 0.5495 (t60) cc_final: 0.5007 (t60) REVERT: B 534 TYR cc_start: 0.6818 (OUTLIER) cc_final: 0.5628 (t80) REVERT: D 348 PHE cc_start: 0.3041 (t80) cc_final: 0.2769 (t80) REVERT: E 382 TRP cc_start: 0.1189 (m100) cc_final: -0.1540 (m100) REVERT: E 454 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8060 (p) REVERT: E 498 GLU cc_start: 0.6535 (mp0) cc_final: 0.6221 (mp0) REVERT: F 487 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: F 518 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6896 (t-90) REVERT: F 553 ASP cc_start: 0.5521 (m-30) cc_final: 0.5242 (m-30) REVERT: G 418 TRP cc_start: 0.7323 (t-100) cc_final: 0.6988 (t-100) REVERT: G 558 LYS cc_start: 0.4246 (mmtt) cc_final: 0.3799 (mtpt) REVERT: H 487 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7540 (pm20) REVERT: I 410 GLU cc_start: 0.7731 (mp0) cc_final: 0.7124 (mp0) REVERT: K 415 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7123 (tm-30) REVERT: K 534 TYR cc_start: 0.6690 (m-80) cc_final: 0.6257 (m-80) REVERT: L 489 MET cc_start: 0.6792 (mmm) cc_final: 0.6094 (mmm) REVERT: L 527 GLU cc_start: 0.6151 (tt0) cc_final: 0.5937 (tt0) outliers start: 78 outliers final: 65 residues processed: 305 average time/residue: 0.1431 time to fit residues: 66.1432 Evaluate side-chains 305 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 235 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 506 MET Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain G residue 413 ILE Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 471 THR Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 529 ASN Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 487 GLN Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain J residue 354 PHE Chi-restraints excluded: chain J residue 375 TYR Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 HIS Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 447 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 503 SER Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain K residue 551 THR Chi-restraints excluded: chain L residue 462 GLU Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 521 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 179 optimal weight: 0.7980 chunk 210 optimal weight: 10.0000 chunk 187 optimal weight: 0.0980 chunk 186 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 chunk 89 optimal weight: 8.9990 chunk 249 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 393 HIS ** G 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN H 450 HIS ** H 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.278947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.238558 restraints weight = 21751.742| |-----------------------------------------------------------------------------| r_work (start): 0.4681 rms_B_bonded: 3.24 r_work: 0.4224 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20520 Z= 0.166 Angle : 0.666 12.178 28104 Z= 0.331 Chirality : 0.047 0.309 3276 Planarity : 0.005 0.060 3612 Dihedral : 5.215 21.520 2748 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.46 % Allowed : 18.42 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.16), residues: 2544 helix: -1.57 (0.25), residues: 352 sheet: -2.83 (0.18), residues: 686 loop : -1.32 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 346 TYR 0.021 0.002 TYR B 500 PHE 0.030 0.002 PHE K 479 TRP 0.025 0.002 TRP A 418 HIS 0.014 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00406 (20496) covalent geometry : angle 0.66529 (28056) SS BOND : bond 0.00380 ( 24) SS BOND : angle 0.88951 ( 48) hydrogen bonds : bond 0.03252 ( 390) hydrogen bonds : angle 7.63695 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 248 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 LYS cc_start: 0.6882 (mmtt) cc_final: 0.6204 (tppt) REVERT: B 488 TRP cc_start: 0.7351 (m100) cc_final: 0.6876 (m100) REVERT: B 534 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.5622 (t80) REVERT: E 454 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.7925 (p) REVERT: E 476 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8083 (p) REVERT: E 498 GLU cc_start: 0.6417 (mp0) cc_final: 0.6136 (mp0) REVERT: F 518 HIS cc_start: 0.7115 (OUTLIER) cc_final: 0.6768 (t-90) REVERT: F 546 ARG cc_start: 0.7472 (tpp-160) cc_final: 0.5825 (ttp-110) REVERT: F 553 ASP cc_start: 0.5814 (m-30) cc_final: 0.5534 (m-30) REVERT: G 418 TRP cc_start: 0.7420 (t-100) cc_final: 0.7092 (t-100) REVERT: G 456 LEU cc_start: 0.8782 (tp) cc_final: 0.8471 (tp) REVERT: G 506 MET cc_start: 0.7740 (mtp) cc_final: 0.7351 (mtp) REVERT: G 558 LYS cc_start: 0.4238 (mmtt) cc_final: 0.3885 (mtpt) REVERT: H 487 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: I 364 LYS cc_start: 0.7673 (mmmt) cc_final: 0.7462 (mmmt) REVERT: I 410 GLU cc_start: 0.7656 (mp0) cc_final: 0.7097 (mp0) REVERT: J 346 ARG cc_start: 0.4990 (tmm160) cc_final: 0.4690 (tmm160) REVERT: K 415 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7239 (mm-30) REVERT: K 534 TYR cc_start: 0.6768 (m-80) cc_final: 0.6437 (m-80) REVERT: L 489 MET cc_start: 0.6745 (mmm) cc_final: 0.6203 (mmm) REVERT: L 527 GLU cc_start: 0.6018 (tt0) cc_final: 0.5792 (tt0) outliers start: 79 outliers final: 63 residues processed: 305 average time/residue: 0.1627 time to fit residues: 74.7596 Evaluate side-chains 299 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 231 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 506 MET Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 471 THR Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain H residue 476 VAL Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain H residue 487 GLN Chi-restraints excluded: chain H residue 501 VAL Chi-restraints excluded: chain H residue 547 VAL Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 455 TYR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 HIS Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 447 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 503 SER Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain L residue 462 GLU Chi-restraints excluded: chain L residue 471 THR Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 510 GLN Chi-restraints excluded: chain L residue 521 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 224 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 182 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 2 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 chunk 113 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 221 optimal weight: 0.0970 chunk 142 optimal weight: 0.0060 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 GLN ** C 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN H 419 ASN H 450 HIS ** H 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN ** I 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 529 ASN L 450 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.281819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.241040 restraints weight = 22090.075| |-----------------------------------------------------------------------------| r_work (start): 0.4680 rms_B_bonded: 3.08 r_work: 0.4267 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20520 Z= 0.142 Angle : 0.654 11.555 28104 Z= 0.324 Chirality : 0.046 0.276 3276 Planarity : 0.005 0.062 3612 Dihedral : 5.075 21.066 2748 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.03 % Allowed : 19.17 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.16), residues: 2544 helix: -1.56 (0.25), residues: 352 sheet: -2.83 (0.19), residues: 650 loop : -1.28 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 467 TYR 0.028 0.002 TYR B 500 PHE 0.028 0.002 PHE K 479 TRP 0.047 0.002 TRP A 418 HIS 0.018 0.001 HIS I 518 Details of bonding type rmsd covalent geometry : bond 0.00346 (20496) covalent geometry : angle 0.65389 (28056) SS BOND : bond 0.00268 ( 24) SS BOND : angle 0.75296 ( 48) hydrogen bonds : bond 0.03209 ( 390) hydrogen bonds : angle 7.23376 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 252 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 LYS cc_start: 0.6811 (mmtt) cc_final: 0.6159 (tppt) REVERT: B 488 TRP cc_start: 0.7295 (m100) cc_final: 0.7070 (m100) REVERT: B 534 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.5699 (t80) REVERT: D 382 TRP cc_start: 0.0138 (m100) cc_final: -0.0432 (m100) REVERT: E 454 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7842 (p) REVERT: E 484 VAL cc_start: 0.7246 (m) cc_final: 0.6857 (m) REVERT: E 498 GLU cc_start: 0.5985 (mp0) cc_final: 0.5673 (mp0) REVERT: F 487 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: F 518 HIS cc_start: 0.7086 (OUTLIER) cc_final: 0.6724 (t-90) REVERT: F 546 ARG cc_start: 0.7343 (tpp-160) cc_final: 0.5817 (ttp-110) REVERT: F 553 ASP cc_start: 0.5922 (m-30) cc_final: 0.5699 (m-30) REVERT: G 418 TRP cc_start: 0.7390 (t-100) cc_final: 0.7136 (t-100) REVERT: G 456 LEU cc_start: 0.8705 (tp) cc_final: 0.8417 (tp) REVERT: G 506 MET cc_start: 0.7093 (mtp) cc_final: 0.6681 (mtp) REVERT: G 558 LYS cc_start: 0.4576 (mmtt) cc_final: 0.4285 (mtpt) REVERT: I 410 GLU cc_start: 0.7566 (mp0) cc_final: 0.7023 (mp0) REVERT: I 501 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7631 (p) REVERT: J 346 ARG cc_start: 0.5186 (tmm160) cc_final: 0.4926 (tmm160) REVERT: K 415 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7068 (tm-30) REVERT: K 503 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8109 (m) REVERT: L 489 MET cc_start: 0.6665 (mmm) cc_final: 0.6105 (mmm) REVERT: L 527 GLU cc_start: 0.5713 (tt0) cc_final: 0.5504 (tt0) outliers start: 69 outliers final: 53 residues processed: 305 average time/residue: 0.1607 time to fit residues: 73.7199 Evaluate side-chains 296 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 475 LEU Chi-restraints excluded: chain E residue 476 VAL Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 348 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain F residue 476 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 487 GLN Chi-restraints excluded: chain F residue 495 LEU Chi-restraints excluded: chain F residue 516 PHE Chi-restraints excluded: chain F residue 518 HIS Chi-restraints excluded: chain F residue 549 GLU Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 471 THR Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 529 ASN Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 518 HIS Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 447 VAL Chi-restraints excluded: chain K residue 489 MET Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 503 SER Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain L residue 462 GLU Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 521 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 63 optimal weight: 20.0000 chunk 78 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 203 optimal weight: 0.0970 chunk 234 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 153 optimal weight: 20.0000 chunk 120 optimal weight: 0.5980 overall best weight: 1.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 393 HIS ** E 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN H 419 ASN ** H 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 529 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.274276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.210511 restraints weight = 22058.230| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 3.39 r_work: 0.4098 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 20520 Z= 0.280 Angle : 0.743 13.604 28104 Z= 0.373 Chirality : 0.049 0.349 3276 Planarity : 0.005 0.065 3612 Dihedral : 5.343 23.097 2748 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.98 % Allowed : 19.52 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.16), residues: 2544 helix: -1.49 (0.26), residues: 371 sheet: -3.00 (0.19), residues: 571 loop : -1.39 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 467 TYR 0.021 0.002 TYR B 500 PHE 0.038 0.002 PHE C 358 TRP 0.039 0.002 TRP A 418 HIS 0.021 0.002 HIS I 518 Details of bonding type rmsd covalent geometry : bond 0.00678 (20496) covalent geometry : angle 0.74227 (28056) SS BOND : bond 0.00715 ( 24) SS BOND : angle 1.03404 ( 48) hydrogen bonds : bond 0.04039 ( 390) hydrogen bonds : angle 7.95984 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4924.78 seconds wall clock time: 85 minutes 29.95 seconds (5129.95 seconds total)