Starting phenix.real_space_refine on Thu Feb 5 21:31:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uo3_64371/02_2026/9uo3_64371.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uo3_64371/02_2026/9uo3_64371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uo3_64371/02_2026/9uo3_64371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uo3_64371/02_2026/9uo3_64371.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uo3_64371/02_2026/9uo3_64371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uo3_64371/02_2026/9uo3_64371.map" } resolution = 3.17 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= 0.008 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 22 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: "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: "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} 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: "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: "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: "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: "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: "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: "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} Time building chain proxies: 4.46, per 1000 atoms: 0.22 Number of scatterers: 19980 At special positions: 0 Unit cell: (58.24, 189.28, 184.8, 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 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 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=2.02 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 I 367 " - pdb=" SG CYS I 426 " distance=2.03 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 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=2.02 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=2.02 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 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 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 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: 1.69 Conformation dependent library (CDL) restraints added in 661.9 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: 44 helices and 62 sheets defined 12.1% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.667A pdb=" N ASN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 466 " --> pdb=" O GLN C 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 462 through 466' Processing helix chain 'C' and resid 524 through 530 removed outlier: 3.716A pdb=" N TRP C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'D' and resid 524 through 530 removed outlier: 3.734A pdb=" N THR D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) Processing helix chain 'K' and resid 353 through 361 Processing helix chain 'K' and resid 414 through 420 Processing helix chain 'K' and resid 462 through 466 removed outlier: 3.906A pdb=" N LEU K 466 " --> pdb=" O GLN K 463 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 500 removed outlier: 3.578A pdb=" N TYR K 500 " --> pdb=" O PRO K 497 " (cutoff:3.500A) Processing helix chain 'K' and resid 524 through 530 removed outlier: 4.322A pdb=" N THR K 530 " --> pdb=" O GLU K 526 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 361 Processing helix chain 'L' and resid 414 through 420 Processing helix chain 'L' and resid 524 through 530 removed outlier: 3.691A pdb=" N THR L 530 " --> pdb=" O GLU L 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 353 through 361 Processing helix chain 'J' and resid 414 through 420 Processing helix chain 'J' and resid 462 through 466 removed outlier: 3.539A pdb=" N ASN J 465 " --> pdb=" O GLU J 462 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU J 466 " --> pdb=" O GLN J 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 462 through 466' Processing helix chain 'J' and resid 524 through 530 removed outlier: 3.795A pdb=" N TRP J 528 " --> pdb=" O SER J 524 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR J 530 " --> pdb=" O GLU J 526 " (cutoff:3.500A) Processing helix chain 'I' and resid 353 through 361 removed outlier: 3.659A pdb=" N THR I 360 " --> pdb=" O SER I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 420 Processing helix chain 'I' and resid 524 through 530 Processing helix chain 'H' and resid 353 through 361 removed outlier: 3.500A pdb=" N THR H 360 " --> pdb=" O SER H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 419 Processing helix chain 'H' and resid 462 through 466 removed outlier: 3.534A pdb=" N ASN H 465 " --> pdb=" O GLU H 462 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU H 466 " --> pdb=" O GLN H 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 462 through 466' Processing helix chain 'H' and resid 525 through 530 removed outlier: 4.312A pdb=" N THR H 530 " --> pdb=" O GLU H 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 553 through 557 removed outlier: 4.208A pdb=" N GLY H 557 " --> pdb=" O LYS H 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 361 Processing helix chain 'G' and resid 414 through 420 Processing helix chain 'G' and resid 524 through 530 removed outlier: 4.234A pdb=" N THR G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 Processing helix chain 'E' and resid 414 through 420 Processing helix chain 'E' and resid 462 through 466 removed outlier: 3.675A pdb=" N ASN E 465 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU E 466 " --> pdb=" O GLN E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 466' Processing helix chain 'E' and resid 524 through 530 removed outlier: 4.215A pdb=" N THR E 530 " --> pdb=" O GLU E 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 420 Processing helix chain 'F' and resid 524 through 530 removed outlier: 4.464A pdb=" N THR F 530 " --> pdb=" O GLU F 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.768A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 525 through 530 removed outlier: 3.948A pdb=" N THR B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.952A pdb=" N THR A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.681A pdb=" N LEU C 365 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 411 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 381 through 383 removed outlier: 3.853A pdb=" N SER C 381 " --> pdb=" O THR C 427 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR C 427 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR C 383 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR C 425 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.798A pdb=" N LEU C 475 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 476 " --> pdb=" O ALA C 517 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N HIS C 518 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA C 504 " --> pdb=" O HIS C 518 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE C 520 " --> pdb=" O THR C 502 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR C 502 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N THR C 522 " --> pdb=" O TYR C 500 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR C 500 " --> pdb=" O THR C 522 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AA5, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.729A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 365 " --> pdb=" O ALA D 411 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA D 411 " --> pdb=" O LEU D 365 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 379 through 383 removed outlier: 3.547A pdb=" N THR D 379 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR D 429 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER D 381 " --> pdb=" O THR D 427 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR D 427 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR D 383 " --> pdb=" O THR D 425 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR D 425 " --> pdb=" O THR D 383 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 453 through 457 Processing sheet with id=AA8, first strand: chain 'D' and resid 453 through 457 Processing sheet with id=AA9, first strand: chain 'D' and resid 493 through 494 removed outlier: 3.727A pdb=" N THR D 535 " --> pdb=" O MET D 489 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 346 through 350 removed outlier: 3.544A pdb=" N THR K 366 " --> pdb=" O ILE K 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 379 through 383 removed outlier: 3.654A pdb=" N THR K 379 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR K 429 " --> pdb=" O THR K 379 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER K 381 " --> pdb=" O THR K 427 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR K 427 " --> pdb=" O SER K 381 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR K 383 " --> pdb=" O THR K 425 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR K 425 " --> pdb=" O THR K 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.658A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR K 515 " --> pdb=" O GLY K 478 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.658A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 493 through 494 removed outlier: 3.621A pdb=" N ARG K 550 " --> pdb=" O CYS K 536 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 346 through 350 removed outlier: 3.514A pdb=" N THR L 366 " --> pdb=" O ILE L 350 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU L 365 " --> pdb=" O ALA L 411 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA L 411 " --> pdb=" O LEU L 365 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 379 through 383 removed outlier: 3.771A pdb=" N THR L 429 " --> pdb=" O THR L 379 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER L 381 " --> pdb=" O THR L 427 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR L 427 " --> pdb=" O SER L 381 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR L 383 " --> pdb=" O THR L 425 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR L 425 " --> pdb=" O THR L 383 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.617A pdb=" N GLY L 478 " --> pdb=" O TYR L 515 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 453 through 457 removed outlier: 3.617A pdb=" N GLY L 478 " --> pdb=" O TYR L 515 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AC2, first strand: chain 'J' and resid 346 through 350 removed outlier: 3.708A pdb=" N ILE J 350 " --> pdb=" O THR J 366 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR J 366 " --> pdb=" O ILE J 350 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU J 365 " --> pdb=" O ALA J 411 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA J 411 " --> pdb=" O LEU J 365 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 381 through 383 removed outlier: 4.038A pdb=" N SER J 381 " --> pdb=" O THR J 427 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR J 427 " --> pdb=" O SER J 381 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR J 383 " --> pdb=" O THR J 425 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 453 through 457 removed outlier: 3.576A pdb=" N THR J 473 " --> pdb=" O LEU J 457 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER J 519 " --> pdb=" O CYS J 474 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR J 515 " --> pdb=" O GLY J 478 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL J 501 " --> pdb=" O ILE J 520 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 453 through 457 removed outlier: 3.576A pdb=" N THR J 473 " --> pdb=" O LEU J 457 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER J 519 " --> pdb=" O CYS J 474 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR J 515 " --> pdb=" O GLY J 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 493 through 494 Processing sheet with id=AC7, first strand: chain 'I' and resid 346 through 350 removed outlier: 3.599A pdb=" N THR I 366 " --> pdb=" O ILE I 350 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU I 365 " --> pdb=" O ALA I 411 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA I 411 " --> pdb=" O LEU I 365 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 379 through 380 removed outlier: 3.768A pdb=" N THR I 429 " --> pdb=" O THR I 379 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 453 through 455 removed outlier: 3.607A pdb=" N LEU I 475 " --> pdb=" O TYR I 455 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR I 515 " --> pdb=" O GLY I 478 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 453 through 455 removed outlier: 3.607A pdb=" N LEU I 475 " --> pdb=" O TYR I 455 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR I 515 " --> pdb=" O GLY I 478 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 493 through 494 Processing sheet with id=AD3, first strand: chain 'H' and resid 346 through 350 removed outlier: 3.623A pdb=" N LEU H 365 " --> pdb=" O ALA H 411 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA H 411 " --> pdb=" O LEU H 365 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 379 through 383 removed outlier: 3.717A pdb=" N THR H 429 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER H 381 " --> pdb=" O THR H 427 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR H 427 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR H 383 " --> pdb=" O THR H 425 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR H 425 " --> pdb=" O THR H 383 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.712A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.712A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 493 through 494 removed outlier: 3.501A pdb=" N ARG H 550 " --> pdb=" O CYS H 536 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 346 through 348 Processing sheet with id=AD9, first strand: chain 'G' and resid 364 through 365 removed outlier: 3.696A pdb=" N LEU G 365 " --> pdb=" O ALA G 411 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA G 411 " --> pdb=" O LEU G 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'G' and resid 379 through 383 removed outlier: 3.730A pdb=" N THR G 429 " --> pdb=" O THR G 379 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER G 381 " --> pdb=" O THR G 427 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR G 427 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR G 383 " --> pdb=" O THR G 425 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR G 425 " --> pdb=" O THR G 383 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 453 through 457 removed outlier: 6.200A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 453 through 457 removed outlier: 6.200A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AE5, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.655A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 381 through 383 removed outlier: 3.903A pdb=" N SER E 381 " --> pdb=" O THR E 427 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR E 427 " --> pdb=" O SER E 381 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR E 383 " --> pdb=" O THR E 425 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR E 425 " --> pdb=" O THR E 383 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.581A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER E 519 " --> pdb=" O CYS E 474 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AE9, first strand: chain 'E' and resid 506 through 507 Processing sheet with id=AF1, first strand: chain 'F' and resid 346 through 348 Processing sheet with id=AF2, first strand: chain 'F' and resid 364 through 365 removed outlier: 3.793A pdb=" N LEU F 365 " --> pdb=" O ALA F 411 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA F 411 " --> pdb=" O LEU F 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 381 through 383 removed outlier: 3.817A pdb=" N SER F 381 " --> pdb=" O THR F 427 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR F 427 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR F 383 " --> pdb=" O THR F 425 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR F 425 " --> pdb=" O THR F 383 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.561A pdb=" N THR F 473 " --> pdb=" O LEU F 457 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 453 through 457 removed outlier: 3.561A pdb=" N THR F 473 " --> pdb=" O LEU F 457 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AF7, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.647A pdb=" N THR B 366 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 411 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 381 through 383 removed outlier: 3.754A pdb=" N SER B 381 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B 427 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 383 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR B 425 " --> pdb=" O THR B 383 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 399 through 400 removed outlier: 4.077A pdb=" N THR B 404 " --> pdb=" O HIS B 400 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.577A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 501 " --> pdb=" O ILE B 520 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.577A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.549A pdb=" N ARG B 550 " --> pdb=" O CYS B 536 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 346 through 350 removed outlier: 3.639A pdb=" N THR A 366 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 365 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 411 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 380 through 383 removed outlier: 3.739A pdb=" N SER A 381 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 427 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 383 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 453 through 457 removed outlier: 6.592A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 453 through 457 removed outlier: 6.592A pdb=" N TYR A 515 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 493 through 494 685 hydrogen bonds defined for protein. 1680 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: 2.81 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6548 1.34 - 1.46: 4499 1.46 - 1.58: 9341 1.58 - 1.70: 0 1.70 - 1.81: 108 Bond restraints: 20496 Sorted by residual: bond pdb=" C SER C 503 " pdb=" N ALA C 504 " ideal model delta sigma weight residual 1.330 1.273 0.057 1.47e-02 4.63e+03 1.49e+01 bond pdb=" C SER J 503 " pdb=" N ALA J 504 " ideal model delta sigma weight residual 1.330 1.275 0.055 1.47e-02 4.63e+03 1.38e+01 bond pdb=" N VAL D 428 " pdb=" CA VAL D 428 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.37e+00 bond pdb=" C SER L 503 " pdb=" N ALA L 504 " ideal model delta sigma weight residual 1.331 1.249 0.082 2.83e-02 1.25e+03 8.35e+00 bond pdb=" C SER H 503 " pdb=" N ALA H 504 " ideal model delta sigma weight residual 1.331 1.274 0.057 2.07e-02 2.33e+03 7.47e+00 ... (remaining 20491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 26875 1.73 - 3.47: 1004 3.47 - 5.20: 138 5.20 - 6.94: 33 6.94 - 8.67: 6 Bond angle restraints: 28056 Sorted by residual: angle pdb=" C LEU E 456 " pdb=" N LEU E 457 " pdb=" CA LEU E 457 " ideal model delta sigma weight residual 121.83 115.51 6.32 1.56e+00 4.11e-01 1.64e+01 angle pdb=" C ASN D 545 " pdb=" N ARG D 546 " pdb=" CA ARG D 546 " ideal model delta sigma weight residual 121.54 129.11 -7.57 1.91e+00 2.74e-01 1.57e+01 angle pdb=" N ASP B 453 " pdb=" CA ASP B 453 " pdb=" C ASP B 453 " ideal model delta sigma weight residual 109.24 102.80 6.44 1.63e+00 3.76e-01 1.56e+01 angle pdb=" CA VAL H 552 " pdb=" C VAL H 552 " pdb=" O VAL H 552 " ideal model delta sigma weight residual 121.72 118.22 3.50 9.60e-01 1.09e+00 1.33e+01 angle pdb=" C SER F 503 " pdb=" N ALA F 504 " pdb=" CA ALA F 504 " ideal model delta sigma weight residual 120.49 115.45 5.04 1.42e+00 4.96e-01 1.26e+01 ... (remaining 28051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10708 18.00 - 36.00: 1341 36.00 - 54.00: 271 54.00 - 72.00: 61 72.00 - 90.00: 51 Dihedral angle restraints: 12432 sinusoidal: 4896 harmonic: 7536 Sorted by residual: dihedral pdb=" CD ARG I 451 " pdb=" NE ARG I 451 " pdb=" CZ ARG I 451 " pdb=" NH1 ARG I 451 " ideal model delta sinusoidal sigma weight residual 0.00 -63.13 63.13 1 1.00e+01 1.00e-02 5.26e+01 dihedral pdb=" CA MET D 506 " pdb=" C MET D 506 " pdb=" N PRO D 507 " pdb=" CA PRO D 507 " ideal model delta harmonic sigma weight residual -180.00 -154.30 -25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PRO J 458 " pdb=" C PRO J 458 " pdb=" N PRO J 459 " pdb=" CA PRO J 459 " ideal model delta harmonic sigma weight residual 180.00 156.69 23.31 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 12429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2328 0.051 - 0.102: 675 0.102 - 0.152: 251 0.152 - 0.203: 20 0.203 - 0.254: 2 Chirality restraints: 3276 Sorted by residual: chirality pdb=" CB THR I 522 " pdb=" CA THR I 522 " pdb=" OG1 THR I 522 " pdb=" CG2 THR I 522 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE D 472 " pdb=" CA ILE D 472 " pdb=" CG1 ILE D 472 " pdb=" CG2 ILE D 472 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+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 2.36 0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 3273 not shown) Planarity restraints: 3612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 451 " 0.986 9.50e-02 1.11e+02 4.42e-01 1.18e+02 pdb=" NE ARG I 451 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG I 451 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG I 451 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I 451 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 461 " 0.644 9.50e-02 1.11e+02 2.89e-01 5.09e+01 pdb=" NE ARG L 461 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG L 461 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG L 461 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG L 461 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS J 518 " -0.024 2.00e-02 2.50e+03 2.06e-02 6.35e+00 pdb=" CG HIS J 518 " 0.043 2.00e-02 2.50e+03 pdb=" ND1 HIS J 518 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS J 518 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS J 518 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS J 518 " -0.009 2.00e-02 2.50e+03 ... (remaining 3609 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 418 2.67 - 3.23: 17610 3.23 - 3.79: 30533 3.79 - 4.34: 38987 4.34 - 4.90: 65123 Nonbonded interactions: 152671 Sorted by model distance: nonbonded pdb=" CD2 LEU H 456 " pdb=" CG2 VAL H 552 " model vdw 2.114 3.880 nonbonded pdb=" OD2 ASP G 453 " pdb=" OH TYR G 455 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR J 383 " pdb=" OG1 THR J 425 " model vdw 2.255 3.040 nonbonded pdb=" O ASP F 553 " pdb=" OG1 THR F 556 " model vdw 2.262 3.040 nonbonded pdb=" O ASP K 553 " pdb=" OG1 THR K 556 " model vdw 2.264 3.040 ... (remaining 152666 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: 0.01 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: 10.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.270 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5627 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 : 0.005 0.082 20520 Z= 0.241 Angle : 0.764 8.671 28104 Z= 0.421 Chirality : 0.053 0.254 3276 Planarity : 0.011 0.442 3612 Dihedral : 17.548 90.000 7440 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 28.46 % Favored : 71.54 % 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: -1.92 (0.16), residues: 2544 helix: -3.04 (0.20), residues: 306 sheet: -0.75 (0.16), residues: 1098 loop : -1.12 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 451 TYR 0.027 0.003 TYR C 534 PHE 0.028 0.002 PHE G 485 TRP 0.021 0.002 TRP G 488 HIS 0.016 0.002 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00528 (20496) covalent geometry : angle 0.76359 (28056) SS BOND : bond 0.00373 ( 24) SS BOND : angle 0.77863 ( 48) hydrogen bonds : bond 0.27762 ( 574) hydrogen bonds : angle 12.05455 ( 1680) *********************** 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 328 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 484 VAL cc_start: 0.7863 (t) cc_final: 0.7590 (t) REVERT: H 361 LYS cc_start: 0.5263 (mmtm) cc_final: 0.4469 (mmtt) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.1458 time to fit residues: 72.4022 Evaluate side-chains 206 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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: 5.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 0.0010 chunk 130 optimal weight: 0.0060 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 HIS ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5202 r_free = 0.5202 target = 0.291940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.255722 restraints weight = 25724.096| |-----------------------------------------------------------------------------| r_work (start): 0.4951 rms_B_bonded: 2.87 r_work: 0.4589 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20520 Z= 0.127 Angle : 0.585 9.497 28104 Z= 0.305 Chirality : 0.047 0.176 3276 Planarity : 0.005 0.050 3612 Dihedral : 4.583 20.289 2748 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.60 % Allowed : 26.40 % Favored : 70.00 % 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: -1.68 (0.16), residues: 2544 helix: -2.70 (0.21), residues: 326 sheet: -0.54 (0.15), residues: 1118 loop : -1.05 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 514 TYR 0.020 0.002 TYR B 534 PHE 0.019 0.001 PHE I 479 TRP 0.029 0.001 TRP B 418 HIS 0.008 0.001 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00281 (20496) covalent geometry : angle 0.58481 (28056) SS BOND : bond 0.00181 ( 24) SS BOND : angle 0.60732 ( 48) hydrogen bonds : bond 0.04332 ( 574) hydrogen bonds : angle 7.44347 ( 1680) *********************** 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 309 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 227 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 484 VAL cc_start: 0.7832 (t) cc_final: 0.7632 (t) REVERT: J 418 TRP cc_start: 0.4216 (OUTLIER) cc_final: 0.2903 (m100) REVERT: I 469 SER cc_start: 0.4956 (OUTLIER) cc_final: 0.4469 (m) REVERT: H 361 LYS cc_start: 0.5355 (mmtm) cc_final: 0.4278 (mmtt) REVERT: G 445 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6231 (mmtp) REVERT: E 518 HIS cc_start: 0.7169 (OUTLIER) cc_final: 0.6562 (t70) REVERT: F 518 HIS cc_start: 0.5893 (p90) cc_final: 0.5325 (p90) REVERT: A 494 PRO cc_start: 0.7598 (Cg_exo) cc_final: 0.7084 (Cg_endo) outliers start: 82 outliers final: 45 residues processed: 289 average time/residue: 0.1250 time to fit residues: 58.8647 Evaluate side-chains 241 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain K residue 453 ASP Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 483 ASP Chi-restraints excluded: chain L residue 472 ILE Chi-restraints excluded: chain L residue 477 THR Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain J residue 393 HIS Chi-restraints excluded: chain J residue 418 TRP Chi-restraints excluded: chain J residue 453 ASP Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 495 LEU Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain I residue 469 SER Chi-restraints excluded: chain I residue 522 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 428 VAL Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 487 GLN Chi-restraints excluded: chain G residue 506 MET Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 441 ILE Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 551 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 135 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 510 GLN ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 450 HIS I 400 HIS I 529 ASN H 490 GLN H 518 HIS G 400 HIS G 529 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.283866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.246757 restraints weight = 25472.039| |-----------------------------------------------------------------------------| r_work (start): 0.4880 rms_B_bonded: 3.52 r_work: 0.4408 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 20520 Z= 0.239 Angle : 0.662 10.437 28104 Z= 0.346 Chirality : 0.050 0.204 3276 Planarity : 0.006 0.053 3612 Dihedral : 5.040 24.072 2748 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 5.18 % Allowed : 26.40 % Favored : 68.42 % 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: -1.68 (0.16), residues: 2544 helix: -2.49 (0.22), residues: 330 sheet: -0.72 (0.15), residues: 1038 loop : -0.89 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 461 TYR 0.022 0.002 TYR E 500 PHE 0.026 0.002 PHE I 479 TRP 0.019 0.002 TRP B 418 HIS 0.015 0.002 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00570 (20496) covalent geometry : angle 0.66216 (28056) SS BOND : bond 0.00403 ( 24) SS BOND : angle 0.70972 ( 48) hydrogen bonds : bond 0.04125 ( 574) hydrogen bonds : angle 7.21537 ( 1680) *********************** 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 318 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 200 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 424 PHE cc_start: 0.2469 (OUTLIER) cc_final: 0.1320 (m-80) REVERT: C 484 VAL cc_start: 0.8057 (t) cc_final: 0.7806 (t) REVERT: K 489 MET cc_start: 0.6100 (tpp) cc_final: 0.5854 (mmt) REVERT: J 418 TRP cc_start: 0.4380 (OUTLIER) cc_final: 0.3269 (m100) REVERT: H 361 LYS cc_start: 0.5385 (mmtm) cc_final: 0.4429 (mmtt) REVERT: G 445 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6474 (mmtp) REVERT: F 518 HIS cc_start: 0.5968 (p90) cc_final: 0.5436 (p90) REVERT: A 506 MET cc_start: 0.6636 (ptp) cc_final: 0.6270 (ptm) outliers start: 118 outliers final: 90 residues processed: 300 average time/residue: 0.1141 time to fit residues: 56.6130 Evaluate side-chains 272 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 179 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain K residue 453 ASP Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 483 ASP Chi-restraints excluded: chain K residue 510 GLN Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain L residue 376 ASP Chi-restraints excluded: chain L residue 402 ASN Chi-restraints excluded: chain L residue 453 ASP Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 528 TRP Chi-restraints excluded: chain L residue 533 THR Chi-restraints excluded: chain L residue 553 ASP Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 418 TRP Chi-restraints excluded: chain J residue 453 ASP Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 536 CYS Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain I residue 368 LEU Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 522 THR Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 522 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: 0.7980 chunk 247 optimal weight: 0.0970 chunk 151 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 168 optimal weight: 30.0000 chunk 190 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 197 optimal weight: 0.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 463 GLN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 529 ASN ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 529 ASN G 529 ASN E 510 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.284747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.249210 restraints weight = 25485.935| |-----------------------------------------------------------------------------| r_work (start): 0.4897 rms_B_bonded: 3.23 r_work: 0.4456 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20520 Z= 0.168 Angle : 0.583 10.801 28104 Z= 0.302 Chirality : 0.047 0.164 3276 Planarity : 0.005 0.043 3612 Dihedral : 4.799 21.872 2748 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 5.31 % Allowed : 26.93 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.16), residues: 2544 helix: -2.32 (0.23), residues: 330 sheet: -0.65 (0.15), residues: 1056 loop : -0.86 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 514 TYR 0.020 0.002 TYR C 534 PHE 0.021 0.002 PHE I 479 TRP 0.014 0.001 TRP B 418 HIS 0.023 0.001 HIS G 400 Details of bonding type rmsd covalent geometry : bond 0.00397 (20496) covalent geometry : angle 0.58334 (28056) SS BOND : bond 0.00240 ( 24) SS BOND : angle 0.53271 ( 48) hydrogen bonds : bond 0.03370 ( 574) hydrogen bonds : angle 6.60552 ( 1680) *********************** 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 331 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 210 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 551 THR cc_start: 0.6899 (t) cc_final: 0.6623 (p) REVERT: K 558 LYS cc_start: 0.3793 (OUTLIER) cc_final: 0.3074 (mmtt) REVERT: L 445 LYS cc_start: 0.4246 (OUTLIER) cc_final: 0.3551 (mmmt) REVERT: J 418 TRP cc_start: 0.4324 (OUTLIER) cc_final: 0.3072 (m100) REVERT: H 361 LYS cc_start: 0.5381 (mmtm) cc_final: 0.4455 (mmtt) REVERT: H 424 PHE cc_start: 0.0724 (OUTLIER) cc_final: -0.1116 (m-80) REVERT: G 445 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6456 (mmtp) REVERT: F 518 HIS cc_start: 0.5898 (p90) cc_final: 0.5312 (p90) REVERT: B 424 PHE cc_start: 0.2631 (OUTLIER) cc_final: 0.2360 (m-80) REVERT: A 506 MET cc_start: 0.6631 (ptp) cc_final: 0.6354 (ptm) REVERT: A 516 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7608 (p90) outliers start: 121 outliers final: 92 residues processed: 315 average time/residue: 0.1202 time to fit residues: 60.9675 Evaluate side-chains 281 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 182 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain K residue 453 ASP Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 483 ASP Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain K residue 558 LYS Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 376 ASP Chi-restraints excluded: chain L residue 402 ASN Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 453 ASP Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 393 HIS Chi-restraints excluded: chain J residue 418 TRP Chi-restraints excluded: chain J residue 453 ASP Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 489 MET Chi-restraints excluded: chain J residue 534 TYR Chi-restraints excluded: chain J residue 536 CYS Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 522 THR Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 400 HIS Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 551 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 116 optimal weight: 0.0010 chunk 232 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 226 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 152 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 118 optimal weight: 0.2980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 463 GLN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 529 ASN ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** 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 = 0.5160 r_free = 0.5160 target = 0.287168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.247697 restraints weight = 25450.024| |-----------------------------------------------------------------------------| r_work (start): 0.4878 rms_B_bonded: 3.38 r_work: 0.4482 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20520 Z= 0.114 Angle : 0.548 12.153 28104 Z= 0.279 Chirality : 0.045 0.149 3276 Planarity : 0.004 0.045 3612 Dihedral : 4.438 19.566 2748 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.09 % Allowed : 27.59 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.37 (0.16), residues: 2544 helix: -2.18 (0.24), residues: 330 sheet: -0.50 (0.15), residues: 1086 loop : -0.75 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 514 TYR 0.018 0.001 TYR C 500 PHE 0.020 0.001 PHE G 424 TRP 0.022 0.001 TRP B 418 HIS 0.009 0.001 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00265 (20496) covalent geometry : angle 0.54819 (28056) SS BOND : bond 0.00158 ( 24) SS BOND : angle 0.53895 ( 48) hydrogen bonds : bond 0.03070 ( 574) hydrogen bonds : angle 5.96695 ( 1680) *********************** 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 317 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 201 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 527 GLU cc_start: 0.6458 (mp0) cc_final: 0.6168 (mt-10) REVERT: D 551 THR cc_start: 0.6958 (t) cc_final: 0.6643 (p) REVERT: K 558 LYS cc_start: 0.3377 (OUTLIER) cc_final: 0.2908 (mmtt) REVERT: L 445 LYS cc_start: 0.4288 (OUTLIER) cc_final: 0.3577 (mmmt) REVERT: J 418 TRP cc_start: 0.4231 (OUTLIER) cc_final: 0.3033 (m100) REVERT: J 495 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5288 (tt) REVERT: H 361 LYS cc_start: 0.5402 (mmtm) cc_final: 0.4469 (mmtt) REVERT: H 498 GLU cc_start: 0.7793 (tp30) cc_final: 0.7579 (tt0) REVERT: H 515 TYR cc_start: 0.7734 (m-80) cc_final: 0.7031 (m-80) REVERT: G 445 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6531 (mmtp) REVERT: F 518 HIS cc_start: 0.5724 (p90) cc_final: 0.5400 (p90) REVERT: A 506 MET cc_start: 0.6532 (ptp) cc_final: 0.6320 (ptm) outliers start: 116 outliers final: 95 residues processed: 299 average time/residue: 0.1223 time to fit residues: 58.9566 Evaluate side-chains 272 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 172 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain K residue 453 ASP Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 483 ASP Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain K residue 558 LYS Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 402 ASN Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 453 ASP Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 528 TRP Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 367 CYS Chi-restraints excluded: chain J residue 393 HIS Chi-restraints excluded: chain J residue 418 TRP Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain J residue 453 ASP Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 495 LEU Chi-restraints excluded: chain J residue 534 TYR Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain I residue 393 HIS Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 522 THR Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 528 TRP Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 506 MET Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 551 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 73 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 203 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 245 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 242 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 HIS ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 ASN G 400 HIS ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** 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 = 0.5152 r_free = 0.5152 target = 0.286311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.249507 restraints weight = 25445.954| |-----------------------------------------------------------------------------| r_work (start): 0.4901 rms_B_bonded: 3.24 r_work: 0.4486 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20520 Z= 0.125 Angle : 0.549 9.697 28104 Z= 0.279 Chirality : 0.046 0.164 3276 Planarity : 0.004 0.043 3612 Dihedral : 4.340 19.136 2748 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 5.61 % Allowed : 27.32 % Favored : 67.06 % 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: -1.35 (0.16), residues: 2544 helix: -2.05 (0.24), residues: 336 sheet: -0.46 (0.16), residues: 954 loop : -0.78 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 514 TYR 0.018 0.001 TYR C 500 PHE 0.019 0.001 PHE I 479 TRP 0.021 0.001 TRP C 382 HIS 0.012 0.001 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00294 (20496) covalent geometry : angle 0.54865 (28056) SS BOND : bond 0.00169 ( 24) SS BOND : angle 0.53249 ( 48) hydrogen bonds : bond 0.02950 ( 574) hydrogen bonds : angle 5.78011 ( 1680) *********************** 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 320 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 192 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 527 GLU cc_start: 0.6446 (mp0) cc_final: 0.6202 (mp0) REVERT: D 551 THR cc_start: 0.7010 (t) cc_final: 0.6683 (p) REVERT: J 418 TRP cc_start: 0.4283 (OUTLIER) cc_final: 0.3132 (m100) REVERT: J 495 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5323 (tt) REVERT: I 518 HIS cc_start: 0.6088 (p90) cc_final: 0.5505 (p90) REVERT: H 361 LYS cc_start: 0.5423 (mmtm) cc_final: 0.4469 (mmtt) REVERT: H 451 ARG cc_start: 0.7880 (ptp90) cc_final: 0.7423 (ptm-80) REVERT: G 445 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6538 (mmtp) REVERT: E 357 ILE cc_start: 0.1512 (mt) cc_final: 0.1307 (mt) REVERT: E 489 MET cc_start: 0.6185 (mtp) cc_final: 0.5955 (mtp) REVERT: F 518 HIS cc_start: 0.5723 (p90) cc_final: 0.5107 (p90) REVERT: A 506 MET cc_start: 0.6555 (ptp) cc_final: 0.6291 (ptm) outliers start: 128 outliers final: 108 residues processed: 299 average time/residue: 0.1195 time to fit residues: 58.6364 Evaluate side-chains 291 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 180 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain K residue 453 ASP Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 483 ASP Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 376 ASP Chi-restraints excluded: chain L residue 402 ASN Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 453 ASP Chi-restraints excluded: chain L residue 484 VAL Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 528 TRP Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 418 TRP Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain J residue 453 ASP Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 495 LEU Chi-restraints excluded: chain J residue 534 TYR Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain J residue 548 THR Chi-restraints excluded: chain I residue 393 HIS Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 522 THR Chi-restraints excluded: chain I residue 529 ASN Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 528 TRP Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 506 MET Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain E residue 360 THR Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 545 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 246 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 GLN K 463 GLN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 ASN G 529 ASN E 463 GLN ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 493 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.283830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.243539 restraints weight = 25396.303| |-----------------------------------------------------------------------------| r_work (start): 0.4831 rms_B_bonded: 3.48 r_work: 0.4414 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20520 Z= 0.184 Angle : 0.597 10.426 28104 Z= 0.307 Chirality : 0.048 0.203 3276 Planarity : 0.005 0.043 3612 Dihedral : 4.629 22.649 2748 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 6.32 % Allowed : 26.80 % Favored : 66.89 % 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: -1.33 (0.16), residues: 2544 helix: -1.93 (0.25), residues: 336 sheet: -0.45 (0.17), residues: 906 loop : -0.79 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 514 TYR 0.018 0.002 TYR C 534 PHE 0.021 0.002 PHE F 479 TRP 0.020 0.001 TRP C 382 HIS 0.026 0.002 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00438 (20496) covalent geometry : angle 0.59679 (28056) SS BOND : bond 0.00271 ( 24) SS BOND : angle 0.59440 ( 48) hydrogen bonds : bond 0.03150 ( 574) hydrogen bonds : angle 6.08100 ( 1680) *********************** 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 329 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 185 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 551 THR cc_start: 0.6980 (t) cc_final: 0.6641 (p) REVERT: K 489 MET cc_start: 0.6071 (tpp) cc_final: 0.5383 (mmt) REVERT: K 558 LYS cc_start: 0.3771 (OUTLIER) cc_final: 0.3082 (mmtt) REVERT: L 445 LYS cc_start: 0.4302 (OUTLIER) cc_final: 0.3595 (mmmt) REVERT: J 418 TRP cc_start: 0.4339 (OUTLIER) cc_final: 0.3209 (m100) REVERT: J 495 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5376 (tt) REVERT: H 361 LYS cc_start: 0.5598 (mmtm) cc_final: 0.4630 (mmtt) REVERT: H 495 LEU cc_start: 0.7706 (tp) cc_final: 0.7500 (mp) REVERT: G 348 PHE cc_start: 0.6015 (m-80) cc_final: 0.5453 (m-10) REVERT: G 445 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6588 (mmtp) REVERT: G 554 LYS cc_start: 0.6622 (mmmt) cc_final: 0.6404 (mppt) REVERT: E 357 ILE cc_start: 0.1733 (mt) cc_final: 0.1492 (mt) REVERT: E 422 GLU cc_start: -0.1526 (OUTLIER) cc_final: -0.2269 (mt-10) REVERT: F 518 HIS cc_start: 0.5824 (p90) cc_final: 0.5232 (p90) REVERT: A 506 MET cc_start: 0.6693 (ptp) cc_final: 0.6436 (ptm) outliers start: 144 outliers final: 127 residues processed: 307 average time/residue: 0.1228 time to fit residues: 62.1869 Evaluate side-chains 303 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 170 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain K residue 453 ASP Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 483 ASP Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain K residue 558 LYS Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 376 ASP Chi-restraints excluded: chain L residue 402 ASN Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 453 ASP Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 528 TRP Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 393 HIS Chi-restraints excluded: chain J residue 418 TRP Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain J residue 453 ASP Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 495 LEU Chi-restraints excluded: chain J residue 534 TYR Chi-restraints excluded: chain J residue 536 CYS Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain J residue 548 THR Chi-restraints excluded: chain J residue 553 ASP Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 368 LEU Chi-restraints excluded: chain I residue 393 HIS Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 522 THR Chi-restraints excluded: chain I residue 529 ASN Chi-restraints excluded: chain I residue 537 VAL Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 528 TRP Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 506 MET Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 545 ASN 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: 20.0000 chunk 78 optimal weight: 4.9990 chunk 230 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 249 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 HIS ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.282985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.245639 restraints weight = 25506.222| |-----------------------------------------------------------------------------| r_work (start): 0.4871 rms_B_bonded: 3.32 r_work: 0.4429 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20520 Z= 0.154 Angle : 0.573 10.643 28104 Z= 0.294 Chirality : 0.047 0.219 3276 Planarity : 0.005 0.062 3612 Dihedral : 4.551 21.786 2748 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 6.49 % Allowed : 26.67 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.16), residues: 2544 helix: -1.83 (0.26), residues: 336 sheet: -0.44 (0.17), residues: 906 loop : -0.75 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 384 TYR 0.019 0.001 TYR K 500 PHE 0.019 0.002 PHE I 479 TRP 0.024 0.001 TRP C 382 HIS 0.014 0.001 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00370 (20496) covalent geometry : angle 0.57349 (28056) SS BOND : bond 0.00206 ( 24) SS BOND : angle 0.50599 ( 48) hydrogen bonds : bond 0.03001 ( 574) hydrogen bonds : angle 5.90602 ( 1680) *********************** 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 329 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 181 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 449 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7427 (mp) REVERT: D 551 THR cc_start: 0.6957 (t) cc_final: 0.6612 (p) REVERT: K 558 LYS cc_start: 0.3467 (OUTLIER) cc_final: 0.3012 (mmtt) REVERT: L 445 LYS cc_start: 0.4226 (OUTLIER) cc_final: 0.3560 (mmmt) REVERT: J 418 TRP cc_start: 0.4330 (OUTLIER) cc_final: 0.3200 (m100) REVERT: J 495 LEU cc_start: 0.6065 (OUTLIER) cc_final: 0.5384 (tt) REVERT: H 361 LYS cc_start: 0.5509 (mmtm) cc_final: 0.4590 (mmtt) REVERT: G 348 PHE cc_start: 0.5785 (m-80) cc_final: 0.5376 (m-10) REVERT: G 445 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6650 (mmtp) REVERT: G 554 LYS cc_start: 0.6666 (mmmt) cc_final: 0.6400 (mppt) REVERT: E 357 ILE cc_start: 0.1951 (mt) cc_final: 0.1666 (mt) REVERT: E 422 GLU cc_start: -0.1529 (OUTLIER) cc_final: -0.2198 (mt-10) REVERT: E 528 TRP cc_start: 0.3973 (t-100) cc_final: 0.1872 (m100) REVERT: A 393 HIS cc_start: 0.4271 (p-80) cc_final: 0.3514 (p90) outliers start: 148 outliers final: 125 residues processed: 303 average time/residue: 0.1138 time to fit residues: 57.3081 Evaluate side-chains 305 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 173 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain K residue 453 ASP Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 483 ASP Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain K residue 533 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain K residue 558 LYS Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 376 ASP Chi-restraints excluded: chain L residue 402 ASN Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 453 ASP Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 528 TRP Chi-restraints excluded: chain L residue 536 CYS Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 418 TRP Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain J residue 453 ASP Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 495 LEU Chi-restraints excluded: chain J residue 534 TYR Chi-restraints excluded: chain J residue 536 CYS Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain J residue 548 THR Chi-restraints excluded: chain J residue 553 ASP Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 368 LEU Chi-restraints excluded: chain I residue 393 HIS Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 522 THR Chi-restraints excluded: chain I residue 529 ASN Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 416 ASP Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 528 TRP Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 506 MET Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 549 GLU Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 528 TRP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 545 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 179 optimal weight: 0.4980 chunk 210 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 249 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 487 GLN ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 ASN G 529 ASN ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** 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 = 0.5131 r_free = 0.5131 target = 0.283922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.253002 restraints weight = 25254.243| |-----------------------------------------------------------------------------| r_work (start): 0.4933 rms_B_bonded: 3.08 r_work: 0.4483 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20520 Z= 0.124 Angle : 0.556 10.669 28104 Z= 0.284 Chirality : 0.046 0.223 3276 Planarity : 0.005 0.049 3612 Dihedral : 4.416 20.330 2748 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 5.96 % Allowed : 27.28 % Favored : 66.75 % 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: -1.17 (0.16), residues: 2544 helix: -1.73 (0.26), residues: 330 sheet: -0.32 (0.16), residues: 924 loop : -0.74 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 384 TYR 0.024 0.001 TYR J 534 PHE 0.018 0.001 PHE I 479 TRP 0.033 0.001 TRP F 418 HIS 0.016 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00294 (20496) covalent geometry : angle 0.55584 (28056) SS BOND : bond 0.00161 ( 24) SS BOND : angle 0.44849 ( 48) hydrogen bonds : bond 0.02894 ( 574) hydrogen bonds : angle 5.68036 ( 1680) *********************** 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 321 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 185 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 449 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7339 (mp) REVERT: D 551 THR cc_start: 0.6994 (t) cc_final: 0.6641 (p) REVERT: K 558 LYS cc_start: 0.3699 (OUTLIER) cc_final: 0.3128 (mmtt) REVERT: L 445 LYS cc_start: 0.4013 (OUTLIER) cc_final: 0.3424 (mmmt) REVERT: J 418 TRP cc_start: 0.4387 (OUTLIER) cc_final: 0.3172 (m100) REVERT: J 495 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5335 (tt) REVERT: I 518 HIS cc_start: 0.6123 (p90) cc_final: 0.5488 (p90) REVERT: H 361 LYS cc_start: 0.5482 (mmtm) cc_final: 0.4601 (mmtt) REVERT: G 348 PHE cc_start: 0.5406 (m-80) cc_final: 0.5205 (m-10) REVERT: G 445 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6546 (mmtp) REVERT: G 554 LYS cc_start: 0.6611 (mmmt) cc_final: 0.6332 (mppt) REVERT: E 357 ILE cc_start: 0.2112 (mt) cc_final: 0.1803 (mt) REVERT: E 422 GLU cc_start: -0.1794 (OUTLIER) cc_final: -0.2251 (mt-10) REVERT: A 393 HIS cc_start: 0.4018 (p-80) cc_final: 0.3266 (p90) outliers start: 136 outliers final: 117 residues processed: 296 average time/residue: 0.1183 time to fit residues: 57.6062 Evaluate side-chains 300 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 176 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 524 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain K residue 453 ASP Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 483 ASP Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 533 THR Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain K residue 558 LYS Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 376 ASP Chi-restraints excluded: chain L residue 402 ASN Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 453 ASP Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 528 TRP Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 418 TRP Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain J residue 453 ASP Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 495 LEU Chi-restraints excluded: chain J residue 536 CYS Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain J residue 548 THR Chi-restraints excluded: chain J residue 553 ASP Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 393 HIS Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 522 THR Chi-restraints excluded: chain I residue 529 ASN Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 506 MET Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 545 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 224 optimal weight: 3.9990 chunk 42 optimal weight: 30.0000 chunk 182 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 221 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 ASN G 529 ASN ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN ** A 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 = 0.5147 r_free = 0.5147 target = 0.282753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.239696 restraints weight = 25460.350| |-----------------------------------------------------------------------------| r_work (start): 0.4770 rms_B_bonded: 4.61 r_work: 0.4334 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.4159 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= 0.167 Angle : 0.602 11.253 28104 Z= 0.307 Chirality : 0.047 0.245 3276 Planarity : 0.005 0.041 3612 Dihedral : 4.639 23.386 2748 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 5.57 % Allowed : 27.50 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.27 (0.16), residues: 2544 helix: -1.72 (0.26), residues: 336 sheet: -0.60 (0.17), residues: 852 loop : -0.66 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 384 TYR 0.023 0.002 TYR K 500 PHE 0.020 0.002 PHE I 479 TRP 0.031 0.002 TRP F 418 HIS 0.015 0.001 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00399 (20496) covalent geometry : angle 0.60177 (28056) SS BOND : bond 0.00274 ( 24) SS BOND : angle 0.51704 ( 48) hydrogen bonds : bond 0.03078 ( 574) hydrogen bonds : angle 5.94745 ( 1680) ********************** 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 312 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 185 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 449 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7551 (mp) REVERT: D 551 THR cc_start: 0.7056 (t) cc_final: 0.6724 (p) REVERT: K 558 LYS cc_start: 0.3591 (OUTLIER) cc_final: 0.3076 (mmtt) REVERT: L 445 LYS cc_start: 0.4281 (OUTLIER) cc_final: 0.3615 (mmmt) REVERT: J 418 TRP cc_start: 0.4352 (OUTLIER) cc_final: 0.3307 (m100) REVERT: H 361 LYS cc_start: 0.5810 (mmtm) cc_final: 0.4888 (mmtt) REVERT: G 348 PHE cc_start: 0.6057 (m-80) cc_final: 0.5664 (m-10) REVERT: G 445 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6737 (mmtp) REVERT: G 554 LYS cc_start: 0.6749 (mmmt) cc_final: 0.6370 (mppt) REVERT: E 357 ILE cc_start: 0.2015 (mt) cc_final: 0.1685 (mt) REVERT: E 422 GLU cc_start: -0.1406 (OUTLIER) cc_final: -0.2216 (mt-10) REVERT: F 364 LYS cc_start: 0.6879 (pttt) cc_final: 0.6607 (ptpp) REVERT: A 393 HIS cc_start: 0.4482 (p-80) cc_final: 0.3701 (p90) outliers start: 127 outliers final: 113 residues processed: 292 average time/residue: 0.1128 time to fit residues: 54.5301 Evaluate side-chains 290 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 171 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 518 HIS Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain D residue 547 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain K residue 453 ASP Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 476 VAL Chi-restraints excluded: chain K residue 483 ASP Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain K residue 547 VAL Chi-restraints excluded: chain K residue 558 LYS Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 376 ASP Chi-restraints excluded: chain L residue 402 ASN Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 453 ASP Chi-restraints excluded: chain L residue 522 THR Chi-restraints excluded: chain L residue 528 TRP Chi-restraints excluded: chain J residue 363 THR Chi-restraints excluded: chain J residue 418 TRP Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain J residue 453 ASP Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 536 CYS Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 547 VAL Chi-restraints excluded: chain J residue 548 THR Chi-restraints excluded: chain J residue 553 ASP Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 393 HIS Chi-restraints excluded: chain I residue 456 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 501 VAL Chi-restraints excluded: chain I residue 522 THR Chi-restraints excluded: chain I residue 529 ASN Chi-restraints excluded: chain I residue 538 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 484 VAL Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 402 ASN Chi-restraints excluded: chain G residue 445 LYS Chi-restraints excluded: chain G residue 453 ASP Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 484 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 547 VAL Chi-restraints excluded: chain G residue 548 THR Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain G residue 553 ASP Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 518 HIS Chi-restraints excluded: chain E residue 519 SER Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 538 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 547 VAL Chi-restraints excluded: chain E residue 552 VAL Chi-restraints excluded: chain F residue 376 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 522 THR Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 549 GLU Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 545 ASN 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: 0.0470 chunk 44 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN K 490 GLN ** K 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 463 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 463 GLN ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 HIS ** I 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 HIS E 450 HIS ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 490 GLN ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5080 r_free = 0.5080 target = 0.277396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.210938 restraints weight = 25469.218| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 4.26 r_work: 0.4209 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.113 20520 Z= 0.356 Angle : 0.799 13.193 28104 Z= 0.418 Chirality : 0.055 0.295 3276 Planarity : 0.006 0.067 3612 Dihedral : 5.700 33.721 2748 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 5.66 % Allowed : 27.50 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.98 % 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: -1.80 (0.16), residues: 2544 helix: -1.77 (0.27), residues: 294 sheet: -1.13 (0.16), residues: 912 loop : -0.99 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 384 TYR 0.034 0.003 TYR E 500 PHE 0.027 0.003 PHE F 479 TRP 0.032 0.003 TRP F 418 HIS 0.023 0.003 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00855 (20496) covalent geometry : angle 0.79832 (28056) SS BOND : bond 0.00791 ( 24) SS BOND : angle 1.05055 ( 48) hydrogen bonds : bond 0.04098 ( 574) hydrogen bonds : angle 7.19962 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5346.84 seconds wall clock time: 92 minutes 24.11 seconds (5544.11 seconds total)