Starting phenix.real_space_refine on Fri Mar 6 03:53:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jpq_9870/03_2026/6jpq_9870.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jpq_9870/03_2026/6jpq_9870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jpq_9870/03_2026/6jpq_9870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jpq_9870/03_2026/6jpq_9870.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jpq_9870/03_2026/6jpq_9870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jpq_9870/03_2026/6jpq_9870.map" } resolution = 4.44 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= -0.034 sd= 0.576 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 132 5.16 5 C 17778 2.51 5 N 4734 2.21 5 O 5124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27768 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4628 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 4.43, per 1000 atoms: 0.16 Number of scatterers: 27768 At special positions: 0 Unit cell: (116.58, 162.14, 152.76, 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 132 16.00 O 5124 8.00 N 4734 7.00 C 17778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6624 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 18 sheets defined 48.6% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 271 through 283 Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 313 through 328 Processing helix chain 'A' and resid 348 through 363 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 386 through 400 removed outlier: 4.128A pdb=" N VAL A 392 " --> pdb=" O HIS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 475 through 495 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.775A pdb=" N PHE A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.996A pdb=" N SER A 533 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 564 removed outlier: 5.832A pdb=" N GLU A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 577 Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.655A pdb=" N LEU A 592 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 635 through 640 Processing helix chain 'A' and resid 646 through 660 Processing helix chain 'A' and resid 679 through 692 removed outlier: 3.674A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 720 Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1146 through 1164 Processing helix chain 'A' and resid 1174 through 1185 Processing helix chain 'B' and resid 271 through 283 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 313 through 328 Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 386 through 400 removed outlier: 4.128A pdb=" N VAL B 392 " --> pdb=" O HIS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 465 through 471 Processing helix chain 'B' and resid 475 through 495 Processing helix chain 'B' and resid 515 through 525 removed outlier: 3.775A pdb=" N PHE B 519 " --> pdb=" O LYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.997A pdb=" N SER B 533 " --> pdb=" O SER B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 564 removed outlier: 5.832A pdb=" N GLU B 551 " --> pdb=" O PRO B 547 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 577 Processing helix chain 'B' and resid 585 through 595 removed outlier: 3.654A pdb=" N LEU B 592 " --> pdb=" O TYR B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 635 through 640 Processing helix chain 'B' and resid 646 through 660 Processing helix chain 'B' and resid 679 through 692 removed outlier: 3.673A pdb=" N GLU B 691 " --> pdb=" O SER B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 720 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 743 through 748 Processing helix chain 'B' and resid 1130 through 1139 Processing helix chain 'B' and resid 1146 through 1164 Processing helix chain 'B' and resid 1174 through 1185 Processing helix chain 'C' and resid 271 through 283 Processing helix chain 'C' and resid 283 through 288 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 313 through 328 Processing helix chain 'C' and resid 348 through 363 Processing helix chain 'C' and resid 372 through 377 Processing helix chain 'C' and resid 386 through 400 removed outlier: 4.129A pdb=" N VAL C 392 " --> pdb=" O HIS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 465 through 471 Processing helix chain 'C' and resid 475 through 495 Processing helix chain 'C' and resid 515 through 525 removed outlier: 3.774A pdb=" N PHE C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 removed outlier: 3.996A pdb=" N SER C 533 " --> pdb=" O SER C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 564 removed outlier: 5.832A pdb=" N GLU C 551 " --> pdb=" O PRO C 547 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP C 555 " --> pdb=" O GLU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 577 Processing helix chain 'C' and resid 585 through 595 removed outlier: 3.655A pdb=" N LEU C 592 " --> pdb=" O TYR C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 625 Processing helix chain 'C' and resid 635 through 640 Processing helix chain 'C' and resid 646 through 660 Processing helix chain 'C' and resid 679 through 692 removed outlier: 3.673A pdb=" N GLU C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 720 Processing helix chain 'C' and resid 733 through 742 Processing helix chain 'C' and resid 743 through 748 Processing helix chain 'C' and resid 1130 through 1139 Processing helix chain 'C' and resid 1146 through 1164 Processing helix chain 'C' and resid 1174 through 1185 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 283 through 288 Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 313 through 328 Processing helix chain 'D' and resid 348 through 363 Processing helix chain 'D' and resid 372 through 377 Processing helix chain 'D' and resid 386 through 400 removed outlier: 4.129A pdb=" N VAL D 392 " --> pdb=" O HIS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 453 Processing helix chain 'D' and resid 465 through 471 Processing helix chain 'D' and resid 475 through 495 Processing helix chain 'D' and resid 515 through 525 removed outlier: 3.774A pdb=" N PHE D 519 " --> pdb=" O LYS D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 533 removed outlier: 3.996A pdb=" N SER D 533 " --> pdb=" O SER D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 564 removed outlier: 5.832A pdb=" N GLU D 551 " --> pdb=" O PRO D 547 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP D 555 " --> pdb=" O GLU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 577 Processing helix chain 'D' and resid 585 through 595 removed outlier: 3.654A pdb=" N LEU D 592 " --> pdb=" O TYR D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 625 Processing helix chain 'D' and resid 635 through 640 Processing helix chain 'D' and resid 646 through 660 Processing helix chain 'D' and resid 679 through 692 removed outlier: 3.673A pdb=" N GLU D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 720 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 743 through 748 Processing helix chain 'D' and resid 1130 through 1139 Processing helix chain 'D' and resid 1146 through 1164 Processing helix chain 'D' and resid 1174 through 1185 Processing helix chain 'E' and resid 271 through 283 Processing helix chain 'E' and resid 283 through 288 Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 313 through 328 Processing helix chain 'E' and resid 348 through 363 Processing helix chain 'E' and resid 372 through 377 Processing helix chain 'E' and resid 386 through 400 removed outlier: 4.129A pdb=" N VAL E 392 " --> pdb=" O HIS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 453 Processing helix chain 'E' and resid 465 through 471 Processing helix chain 'E' and resid 475 through 495 Processing helix chain 'E' and resid 515 through 525 removed outlier: 3.774A pdb=" N PHE E 519 " --> pdb=" O LYS E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 533 removed outlier: 3.995A pdb=" N SER E 533 " --> pdb=" O SER E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 564 removed outlier: 5.831A pdb=" N GLU E 551 " --> pdb=" O PRO E 547 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP E 555 " --> pdb=" O GLU E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 577 Processing helix chain 'E' and resid 585 through 595 removed outlier: 3.653A pdb=" N LEU E 592 " --> pdb=" O TYR E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 625 Processing helix chain 'E' and resid 635 through 640 Processing helix chain 'E' and resid 646 through 660 Processing helix chain 'E' and resid 679 through 692 removed outlier: 3.673A pdb=" N GLU E 691 " --> pdb=" O SER E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 720 Processing helix chain 'E' and resid 733 through 741 Processing helix chain 'E' and resid 743 through 748 Processing helix chain 'E' and resid 1130 through 1139 Processing helix chain 'E' and resid 1146 through 1164 Processing helix chain 'E' and resid 1174 through 1185 Processing helix chain 'F' and resid 271 through 283 Processing helix chain 'F' and resid 283 through 288 Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 313 through 328 Processing helix chain 'F' and resid 348 through 363 Processing helix chain 'F' and resid 372 through 377 Processing helix chain 'F' and resid 386 through 400 removed outlier: 4.128A pdb=" N VAL F 392 " --> pdb=" O HIS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 453 Processing helix chain 'F' and resid 465 through 471 Processing helix chain 'F' and resid 475 through 495 Processing helix chain 'F' and resid 515 through 525 removed outlier: 3.774A pdb=" N PHE F 519 " --> pdb=" O LYS F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 533 removed outlier: 3.995A pdb=" N SER F 533 " --> pdb=" O SER F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 564 removed outlier: 5.832A pdb=" N GLU F 551 " --> pdb=" O PRO F 547 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA F 552 " --> pdb=" O LEU F 548 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP F 555 " --> pdb=" O GLU F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 577 Processing helix chain 'F' and resid 585 through 595 removed outlier: 3.654A pdb=" N LEU F 592 " --> pdb=" O TYR F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 617 through 625 Processing helix chain 'F' and resid 635 through 640 Processing helix chain 'F' and resid 646 through 660 Processing helix chain 'F' and resid 679 through 692 removed outlier: 3.674A pdb=" N GLU F 691 " --> pdb=" O SER F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 720 Processing helix chain 'F' and resid 733 through 741 Processing helix chain 'F' and resid 743 through 748 Processing helix chain 'F' and resid 1130 through 1139 Processing helix chain 'F' and resid 1146 through 1164 Processing helix chain 'F' and resid 1174 through 1185 Processing sheet with id=AA1, first strand: chain 'A' and resid 332 through 337 removed outlier: 6.796A pdb=" N SER A 332 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE A 369 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR A 334 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP A 371 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG A 336 " --> pdb=" O ASP A 371 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER A 366 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE A 411 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 368 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA A 413 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 370 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL A 303 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 578 through 579 removed outlier: 3.542A pdb=" N LYS B 762 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 630 through 633 removed outlier: 6.984A pdb=" N SER A 664 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU A 702 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 666 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU A 704 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE A 668 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 762 through 763 removed outlier: 3.663A pdb=" N LYS A 762 " --> pdb=" O ASP F 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 332 through 337 removed outlier: 6.797A pdb=" N SER B 332 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE B 369 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR B 334 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ASP B 371 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG B 336 " --> pdb=" O ASP B 371 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER B 366 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ILE B 411 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 368 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA B 413 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE B 370 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL B 303 " --> pdb=" O GLY B 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 579 removed outlier: 3.604A pdb=" N LYS C 762 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 630 through 633 removed outlier: 6.984A pdb=" N SER B 664 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU B 702 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 666 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LEU B 704 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE B 668 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 332 through 337 removed outlier: 6.796A pdb=" N SER C 332 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE C 369 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR C 334 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP C 371 " --> pdb=" O TYR C 334 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG C 336 " --> pdb=" O ASP C 371 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER C 366 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE C 411 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE C 368 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA C 413 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE C 370 " --> pdb=" O ALA C 413 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL C 303 " --> pdb=" O GLY C 412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 578 through 579 Processing sheet with id=AB1, first strand: chain 'C' and resid 630 through 633 removed outlier: 6.984A pdb=" N SER C 664 " --> pdb=" O LEU C 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU C 702 " --> pdb=" O SER C 664 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 666 " --> pdb=" O LEU C 702 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU C 704 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE C 668 " --> pdb=" O LEU C 704 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 332 through 337 removed outlier: 6.796A pdb=" N SER D 332 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE D 369 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR D 334 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP D 371 " --> pdb=" O TYR D 334 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG D 336 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER D 366 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE D 411 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE D 368 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ALA D 413 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE D 370 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL D 303 " --> pdb=" O GLY D 412 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 578 through 579 removed outlier: 3.511A pdb=" N LYS E 762 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 630 through 633 removed outlier: 6.983A pdb=" N SER D 664 " --> pdb=" O LEU D 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU D 702 " --> pdb=" O SER D 664 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 666 " --> pdb=" O LEU D 702 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU D 704 " --> pdb=" O ILE D 666 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE D 668 " --> pdb=" O LEU D 704 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 332 through 337 removed outlier: 6.796A pdb=" N SER E 332 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE E 369 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR E 334 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP E 371 " --> pdb=" O TYR E 334 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG E 336 " --> pdb=" O ASP E 371 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER E 366 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE E 411 " --> pdb=" O SER E 366 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE E 368 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ALA E 413 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE E 370 " --> pdb=" O ALA E 413 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL E 303 " --> pdb=" O GLY E 412 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 578 through 579 removed outlier: 3.659A pdb=" N LYS F 762 " --> pdb=" O ASP E 579 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 630 through 633 removed outlier: 6.984A pdb=" N SER E 664 " --> pdb=" O LEU E 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU E 702 " --> pdb=" O SER E 664 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 666 " --> pdb=" O LEU E 702 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU E 704 " --> pdb=" O ILE E 666 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE E 668 " --> pdb=" O LEU E 704 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 332 through 337 removed outlier: 6.795A pdb=" N SER F 332 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N PHE F 369 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR F 334 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP F 371 " --> pdb=" O TYR F 334 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG F 336 " --> pdb=" O ASP F 371 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER F 366 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE F 411 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE F 368 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA F 413 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE F 370 " --> pdb=" O ALA F 413 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL F 303 " --> pdb=" O GLY F 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 630 through 633 removed outlier: 6.983A pdb=" N SER F 664 " --> pdb=" O LEU F 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU F 702 " --> pdb=" O SER F 664 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 666 " --> pdb=" O LEU F 702 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU F 704 " --> pdb=" O ILE F 666 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE F 668 " --> pdb=" O LEU F 704 " (cutoff:3.500A) 1115 hydrogen bonds defined for protein. 3306 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: 5.07 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8895 1.34 - 1.46: 5310 1.46 - 1.57: 13971 1.57 - 1.69: 0 1.69 - 1.81: 228 Bond restraints: 28404 Sorted by residual: bond pdb=" C LEU A 284 " pdb=" N PRO A 285 " ideal model delta sigma weight residual 1.335 1.365 -0.031 1.19e-02 7.06e+03 6.68e+00 bond pdb=" C LEU E 284 " pdb=" N PRO E 285 " ideal model delta sigma weight residual 1.335 1.365 -0.031 1.19e-02 7.06e+03 6.65e+00 bond pdb=" C LEU C 284 " pdb=" N PRO C 285 " ideal model delta sigma weight residual 1.335 1.365 -0.031 1.19e-02 7.06e+03 6.61e+00 bond pdb=" C LEU F 284 " pdb=" N PRO F 285 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.19e-02 7.06e+03 6.56e+00 bond pdb=" C LEU D 284 " pdb=" N PRO D 285 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.19e-02 7.06e+03 6.46e+00 ... (remaining 28399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 37126 2.68 - 5.36: 1175 5.36 - 8.04: 147 8.04 - 10.72: 6 10.72 - 13.40: 12 Bond angle restraints: 38466 Sorted by residual: angle pdb=" C GLN F 615 " pdb=" N THR F 616 " pdb=" CA THR F 616 " ideal model delta sigma weight residual 122.61 129.85 -7.24 1.56e+00 4.11e-01 2.15e+01 angle pdb=" C GLN A 615 " pdb=" N THR A 616 " pdb=" CA THR A 616 " ideal model delta sigma weight residual 122.61 129.82 -7.21 1.56e+00 4.11e-01 2.14e+01 angle pdb=" C GLN B 615 " pdb=" N THR B 616 " pdb=" CA THR B 616 " ideal model delta sigma weight residual 122.61 129.82 -7.21 1.56e+00 4.11e-01 2.13e+01 angle pdb=" C GLN C 615 " pdb=" N THR C 616 " pdb=" CA THR C 616 " ideal model delta sigma weight residual 122.61 129.81 -7.20 1.56e+00 4.11e-01 2.13e+01 angle pdb=" C GLN D 615 " pdb=" N THR D 616 " pdb=" CA THR D 616 " ideal model delta sigma weight residual 122.61 129.79 -7.18 1.56e+00 4.11e-01 2.12e+01 ... (remaining 38461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.08: 16102 15.08 - 30.16: 1136 30.16 - 45.25: 264 45.25 - 60.33: 30 60.33 - 75.41: 54 Dihedral angle restraints: 17586 sinusoidal: 7422 harmonic: 10164 Sorted by residual: dihedral pdb=" CA GLN C 298 " pdb=" C GLN C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta harmonic sigma weight residual -180.00 -121.96 -58.04 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA GLN E 298 " pdb=" C GLN E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta harmonic sigma weight residual -180.00 -122.01 -57.99 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA GLN F 298 " pdb=" C GLN F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta harmonic sigma weight residual -180.00 -122.02 -57.98 0 5.00e+00 4.00e-02 1.34e+02 ... (remaining 17583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2563 0.047 - 0.094: 1236 0.094 - 0.141: 394 0.141 - 0.189: 77 0.189 - 0.236: 32 Chirality restraints: 4302 Sorted by residual: chirality pdb=" CA THR C1132 " pdb=" N THR C1132 " pdb=" C THR C1132 " pdb=" CB THR C1132 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA THR F1132 " pdb=" N THR F1132 " pdb=" C THR F1132 " pdb=" CB THR F1132 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA THR B1132 " pdb=" N THR B1132 " pdb=" C THR B1132 " pdb=" CB THR B1132 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4299 not shown) Planarity restraints: 4950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 298 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B 299 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 299 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 299 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 298 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO D 299 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO D 299 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 299 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 298 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO F 299 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO F 299 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 299 " -0.046 5.00e-02 4.00e+02 ... (remaining 4947 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 2938 2.74 - 3.28: 28400 3.28 - 3.82: 48358 3.82 - 4.36: 56889 4.36 - 4.90: 89636 Nonbonded interactions: 226221 Sorted by model distance: nonbonded pdb=" OG SER A 393 " pdb=" O LYS B 337 " model vdw 2.195 3.040 nonbonded pdb=" O LYS A 337 " pdb=" OG SER F 393 " model vdw 2.195 3.040 nonbonded pdb=" O LEU C1137 " pdb=" OG SER C1141 " model vdw 2.241 3.040 nonbonded pdb=" O LEU D1137 " pdb=" OG SER D1141 " model vdw 2.241 3.040 nonbonded pdb=" O LEU E1137 " pdb=" OG SER E1141 " model vdw 2.241 3.040 ... (remaining 226216 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 22.900 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.006 0.060 28404 Z= 0.314 Angle : 1.131 13.399 38466 Z= 0.633 Chirality : 0.061 0.236 4302 Planarity : 0.009 0.086 4950 Dihedral : 12.175 75.410 10962 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.57 % Allowed : 5.17 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 4.76 % 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: -5.01 (0.11), residues: 3438 helix: -3.34 (0.08), residues: 1548 sheet: -1.76 (0.23), residues: 384 loop : -3.68 (0.13), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 599 TYR 0.024 0.004 TYR F 601 PHE 0.023 0.003 PHE C 436 TRP 0.018 0.003 TRP E 455 HIS 0.013 0.004 HIS F 630 Details of bonding type rmsd covalent geometry : bond 0.00642 (28404) covalent geometry : angle 1.13123 (38466) hydrogen bonds : bond 0.13123 ( 1115) hydrogen bonds : angle 8.93687 ( 3306) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 798 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6436 (tm-30) REVERT: A 316 MET cc_start: 0.9590 (mmm) cc_final: 0.9335 (mmm) REVERT: A 410 ILE cc_start: 0.8745 (mt) cc_final: 0.8327 (mt) REVERT: A 640 LEU cc_start: 0.9529 (mm) cc_final: 0.9277 (mm) REVERT: A 716 LEU cc_start: 0.9775 (mt) cc_final: 0.9379 (pp) REVERT: A 718 GLU cc_start: 0.9449 (OUTLIER) cc_final: 0.9199 (pm20) REVERT: A 719 TRP cc_start: 0.9456 (m-10) cc_final: 0.9094 (m-90) REVERT: A 729 LEU cc_start: 0.9411 (mm) cc_final: 0.9194 (mt) REVERT: A 741 PHE cc_start: 0.9592 (m-80) cc_final: 0.8896 (m-80) REVERT: A 1152 HIS cc_start: 0.9633 (m90) cc_final: 0.9360 (m-70) REVERT: B 305 PHE cc_start: 0.9684 (m-10) cc_final: 0.9333 (m-80) REVERT: B 318 ARG cc_start: 0.9418 (tpm170) cc_final: 0.9184 (tpp-160) REVERT: B 320 LEU cc_start: 0.9557 (mt) cc_final: 0.9093 (mt) REVERT: B 351 ARG cc_start: 0.9043 (ptm-80) cc_final: 0.8784 (ttp80) REVERT: B 442 ASP cc_start: 0.9708 (p0) cc_final: 0.9497 (p0) REVERT: B 519 PHE cc_start: 0.9617 (m-80) cc_final: 0.9209 (m-80) REVERT: B 549 LEU cc_start: 0.9596 (mt) cc_final: 0.9249 (mp) REVERT: B 564 MET cc_start: 0.9405 (ttp) cc_final: 0.8994 (ppp) REVERT: B 584 ASN cc_start: 0.8133 (t0) cc_final: 0.7846 (m-40) REVERT: B 630 HIS cc_start: 0.8006 (t-90) cc_final: 0.7605 (t-90) REVERT: B 636 MET cc_start: 0.9473 (pmm) cc_final: 0.8818 (mmt) REVERT: B 727 TYR cc_start: 0.8688 (t80) cc_final: 0.8487 (t80) REVERT: B 1185 MET cc_start: 0.9234 (mtt) cc_final: 0.8994 (mmm) REVERT: C 320 LEU cc_start: 0.8795 (mt) cc_final: 0.7942 (mt) REVERT: C 352 GLN cc_start: 0.9364 (mp10) cc_final: 0.9092 (mt0) REVERT: C 399 MET cc_start: 0.9723 (mmt) cc_final: 0.9506 (mmp) REVERT: C 480 ARG cc_start: 0.9504 (mmt90) cc_final: 0.9060 (mmm-85) REVERT: C 671 ILE cc_start: 0.9247 (mt) cc_final: 0.9013 (mt) REVERT: C 690 LEU cc_start: 0.9409 (mt) cc_final: 0.9159 (mt) REVERT: D 281 MET cc_start: 0.7781 (mmt) cc_final: 0.7408 (mmm) REVERT: D 369 PHE cc_start: 0.8614 (m-10) cc_final: 0.8261 (m-80) REVERT: D 399 MET cc_start: 0.9578 (mmt) cc_final: 0.9357 (mmt) REVERT: D 430 PHE cc_start: 0.8892 (m-10) cc_final: 0.8688 (m-80) REVERT: D 432 ARG cc_start: 0.8522 (mmt180) cc_final: 0.8320 (mtm-85) REVERT: D 480 ARG cc_start: 0.9694 (mmt90) cc_final: 0.9406 (tpp80) REVERT: D 591 ARG cc_start: 0.9291 (mtt90) cc_final: 0.9014 (mtt-85) REVERT: D 636 MET cc_start: 0.9748 (pmm) cc_final: 0.9534 (pmm) REVERT: E 288 TYR cc_start: 0.8931 (m-10) cc_final: 0.8681 (m-10) REVERT: E 371 ASP cc_start: 0.9579 (m-30) cc_final: 0.9324 (p0) REVERT: E 399 MET cc_start: 0.9018 (mmt) cc_final: 0.8695 (mmt) REVERT: E 415 ASN cc_start: 0.8594 (t160) cc_final: 0.7765 (t160) REVERT: E 430 PHE cc_start: 0.7710 (m-10) cc_final: 0.7094 (m-10) REVERT: E 479 LEU cc_start: 0.9557 (mt) cc_final: 0.9313 (mt) REVERT: E 591 ARG cc_start: 0.8611 (mtt90) cc_final: 0.7976 (mmp80) REVERT: E 592 LEU cc_start: 0.9338 (pt) cc_final: 0.8977 (pt) REVERT: E 653 HIS cc_start: 0.9662 (m170) cc_final: 0.9417 (m-70) REVERT: E 701 PHE cc_start: 0.9281 (t80) cc_final: 0.8679 (t80) REVERT: F 298 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8334 (tp40) REVERT: F 356 LEU cc_start: 0.9661 (tt) cc_final: 0.9403 (mt) REVERT: F 432 ARG cc_start: 0.9226 (mmt180) cc_final: 0.8860 (mtm-85) REVERT: F 519 PHE cc_start: 0.9522 (m-80) cc_final: 0.9161 (t80) REVERT: F 523 MET cc_start: 0.8556 (mmm) cc_final: 0.7334 (mmp) REVERT: F 592 LEU cc_start: 0.9703 (pt) cc_final: 0.9467 (pt) REVERT: F 686 PHE cc_start: 0.9379 (t80) cc_final: 0.9073 (t80) REVERT: F 689 MET cc_start: 0.9614 (mmm) cc_final: 0.9331 (mmm) REVERT: F 704 LEU cc_start: 0.9359 (tp) cc_final: 0.9146 (tp) REVERT: F 720 PHE cc_start: 0.9216 (m-80) cc_final: 0.9010 (m-80) REVERT: F 738 ILE cc_start: 0.9468 (pt) cc_final: 0.9268 (mm) REVERT: F 741 PHE cc_start: 0.9219 (m-80) cc_final: 0.8635 (m-80) outliers start: 18 outliers final: 2 residues processed: 812 average time/residue: 0.2300 time to fit residues: 273.7273 Evaluate side-chains 522 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 519 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 HIS A 384 GLN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 661 HIS A1154 HIS ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 384 GLN B 454 ASN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B 624 GLN ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN C1152 HIS D 384 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN D 506 GLN D 589 GLN D 645 GLN D 653 HIS ** D 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 GLN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 589 GLN E 653 HIS F 384 GLN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN F 506 GLN F 589 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.091526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.065785 restraints weight = 174416.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.067209 restraints weight = 136741.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.068379 restraints weight = 113213.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.069223 restraints weight = 97269.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.069979 restraints weight = 86208.436| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28404 Z= 0.134 Angle : 0.730 12.836 38466 Z= 0.373 Chirality : 0.046 0.209 4302 Planarity : 0.007 0.107 4950 Dihedral : 6.790 44.972 3762 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.42 % Allowed : 3.74 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.13), residues: 3438 helix: -1.79 (0.12), residues: 1530 sheet: -1.35 (0.25), residues: 384 loop : -3.22 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 480 TYR 0.020 0.001 TYR B 601 PHE 0.021 0.002 PHE B 305 TRP 0.028 0.001 TRP B 345 HIS 0.016 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00288 (28404) covalent geometry : angle 0.72951 (38466) hydrogen bonds : bond 0.04062 ( 1115) hydrogen bonds : angle 5.30787 ( 3306) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 692 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7808 (mtmm) REVERT: A 304 LEU cc_start: 0.7795 (mm) cc_final: 0.7292 (tt) REVERT: A 316 MET cc_start: 0.9570 (mmm) cc_final: 0.9269 (mmm) REVERT: A 335 MET cc_start: 0.7772 (mmt) cc_final: 0.7506 (mmp) REVERT: A 371 ASP cc_start: 0.9512 (t0) cc_final: 0.9111 (m-30) REVERT: A 402 MET cc_start: 0.7218 (mtp) cc_final: 0.6957 (mtp) REVERT: A 410 ILE cc_start: 0.8714 (mt) cc_final: 0.8001 (mt) REVERT: A 424 LEU cc_start: 0.8965 (mp) cc_final: 0.8307 (mp) REVERT: A 548 LEU cc_start: 0.9265 (mm) cc_final: 0.9046 (mm) REVERT: A 631 VAL cc_start: 0.9136 (t) cc_final: 0.8931 (t) REVERT: A 653 HIS cc_start: 0.9375 (m-70) cc_final: 0.8975 (m-70) REVERT: A 665 ILE cc_start: 0.9173 (mp) cc_final: 0.8890 (mp) REVERT: A 701 PHE cc_start: 0.9012 (t80) cc_final: 0.8810 (t80) REVERT: A 1152 HIS cc_start: 0.9701 (m90) cc_final: 0.9212 (m-70) REVERT: A 1157 LEU cc_start: 0.9495 (mm) cc_final: 0.9245 (pp) REVERT: B 288 TYR cc_start: 0.9276 (m-80) cc_final: 0.8931 (m-80) REVERT: B 398 LEU cc_start: 0.9535 (mp) cc_final: 0.9179 (mp) REVERT: B 399 MET cc_start: 0.9090 (mmp) cc_final: 0.8800 (mmp) REVERT: B 402 MET cc_start: 0.6172 (mtt) cc_final: 0.5783 (mtm) REVERT: B 519 PHE cc_start: 0.9597 (m-80) cc_final: 0.9238 (m-80) REVERT: B 521 MET cc_start: 0.9570 (mtm) cc_final: 0.9174 (mtp) REVERT: B 545 LEU cc_start: 0.9754 (mp) cc_final: 0.9484 (tp) REVERT: B 564 MET cc_start: 0.9176 (ttp) cc_final: 0.8921 (ppp) REVERT: B 584 ASN cc_start: 0.8493 (t0) cc_final: 0.8084 (m-40) REVERT: B 635 ASP cc_start: 0.9803 (t0) cc_final: 0.9528 (t0) REVERT: B 653 HIS cc_start: 0.9450 (m90) cc_final: 0.9193 (m-70) REVERT: B 1185 MET cc_start: 0.9330 (mtt) cc_final: 0.9116 (mmt) REVERT: C 266 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8459 (tm-30) REVERT: C 441 ARG cc_start: 0.8882 (tpp80) cc_final: 0.8630 (tpp80) REVERT: C 442 ASP cc_start: 0.9476 (p0) cc_final: 0.9206 (p0) REVERT: C 480 ARG cc_start: 0.9582 (mmt90) cc_final: 0.9058 (mmm-85) REVERT: C 521 MET cc_start: 0.9749 (mtm) cc_final: 0.9463 (mtp) REVERT: C 636 MET cc_start: 0.9364 (pmm) cc_final: 0.9096 (pmm) REVERT: C 665 ILE cc_start: 0.9436 (mm) cc_final: 0.9198 (mm) REVERT: C 765 VAL cc_start: 0.8879 (m) cc_final: 0.8639 (p) REVERT: C 1152 HIS cc_start: 0.9334 (m170) cc_final: 0.8924 (m-70) REVERT: D 281 MET cc_start: 0.7733 (mmt) cc_final: 0.7515 (mmp) REVERT: D 416 ARG cc_start: 0.8979 (pmt170) cc_final: 0.8668 (pmt-80) REVERT: D 430 PHE cc_start: 0.8892 (m-10) cc_final: 0.8591 (m-80) REVERT: D 591 ARG cc_start: 0.9300 (mtt90) cc_final: 0.8774 (mtm180) REVERT: D 689 MET cc_start: 0.9426 (mmp) cc_final: 0.9216 (mmm) REVERT: D 1184 PHE cc_start: 0.8645 (t80) cc_final: 0.8046 (t80) REVERT: E 371 ASP cc_start: 0.9553 (m-30) cc_final: 0.9330 (t0) REVERT: E 479 LEU cc_start: 0.9483 (mt) cc_final: 0.9270 (mt) REVERT: E 591 ARG cc_start: 0.8577 (mtt90) cc_final: 0.7976 (mmp80) REVERT: E 592 LEU cc_start: 0.9326 (pt) cc_final: 0.8982 (pt) REVERT: E 635 ASP cc_start: 0.9608 (t70) cc_final: 0.9387 (t0) REVERT: E 653 HIS cc_start: 0.9759 (m-70) cc_final: 0.9442 (m-70) REVERT: E 697 ASP cc_start: 0.9391 (t0) cc_final: 0.9136 (t0) REVERT: E 701 PHE cc_start: 0.9244 (t80) cc_final: 0.8480 (t80) REVERT: F 274 TYR cc_start: 0.9425 (m-10) cc_final: 0.9191 (m-10) REVERT: F 351 ARG cc_start: 0.8216 (mmp80) cc_final: 0.7785 (mmp80) REVERT: F 370 PHE cc_start: 0.8955 (m-80) cc_final: 0.8690 (m-80) REVERT: F 432 ARG cc_start: 0.9008 (mmt180) cc_final: 0.8776 (mpp-170) REVERT: F 519 PHE cc_start: 0.9483 (m-80) cc_final: 0.9125 (m-80) REVERT: F 527 ILE cc_start: 0.8904 (pt) cc_final: 0.8702 (tt) REVERT: F 584 ASN cc_start: 0.8490 (t0) cc_final: 0.8009 (p0) REVERT: F 592 LEU cc_start: 0.9631 (pt) cc_final: 0.9428 (pt) REVERT: F 601 TYR cc_start: 0.7923 (t80) cc_final: 0.7665 (t80) REVERT: F 622 ILE cc_start: 0.8912 (pt) cc_final: 0.8677 (pt) REVERT: F 636 MET cc_start: 0.9051 (mpp) cc_final: 0.8614 (mmt) REVERT: F 657 GLU cc_start: 0.9418 (mp0) cc_final: 0.9067 (mp0) REVERT: F 674 TRP cc_start: 0.9219 (t60) cc_final: 0.8778 (t60) REVERT: F 689 MET cc_start: 0.9713 (mmm) cc_final: 0.9268 (mmm) REVERT: F 697 ASP cc_start: 0.8649 (m-30) cc_final: 0.8256 (m-30) REVERT: F 727 TYR cc_start: 0.8329 (t80) cc_final: 0.8019 (t80) REVERT: F 738 ILE cc_start: 0.9596 (pt) cc_final: 0.9314 (mm) REVERT: F 741 PHE cc_start: 0.9250 (m-80) cc_final: 0.8719 (m-80) REVERT: F 1154 HIS cc_start: 0.9097 (t70) cc_final: 0.8378 (t-90) REVERT: F 1179 ARG cc_start: 0.9563 (ptt180) cc_final: 0.9303 (mtm110) outliers start: 13 outliers final: 1 residues processed: 701 average time/residue: 0.2181 time to fit residues: 226.7288 Evaluate side-chains 502 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 501 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 333 optimal weight: 8.9990 chunk 282 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 260 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 320 optimal weight: 9.9990 chunk 264 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN A 506 GLN A 589 GLN A 615 GLN A 661 HIS ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN B 506 GLN ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN C 388 HIS ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN C 506 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 HIS ** D 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 GLN E 489 ASN E 497 GLN E 506 GLN E 661 HIS ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 661 HIS F 742 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.085623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.060448 restraints weight = 174896.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.061764 restraints weight = 135656.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.062651 restraints weight = 111813.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.063439 restraints weight = 97581.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.063926 restraints weight = 87051.499| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28404 Z= 0.178 Angle : 0.746 16.048 38466 Z= 0.384 Chirality : 0.047 0.207 4302 Planarity : 0.007 0.077 4950 Dihedral : 6.453 44.107 3762 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.22 % Allowed : 4.34 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.13), residues: 3438 helix: -1.34 (0.12), residues: 1608 sheet: -1.35 (0.26), residues: 396 loop : -3.10 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 429 TYR 0.025 0.002 TYR A1158 PHE 0.020 0.002 PHE B 436 TRP 0.025 0.002 TRP A 674 HIS 0.012 0.002 HIS E 661 Details of bonding type rmsd covalent geometry : bond 0.00374 (28404) covalent geometry : angle 0.74586 (38466) hydrogen bonds : bond 0.03968 ( 1115) hydrogen bonds : angle 5.13164 ( 3306) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 590 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7846 (ttpp) REVERT: A 283 MET cc_start: 0.9211 (ptt) cc_final: 0.8725 (ptt) REVERT: A 314 THR cc_start: 0.9230 (p) cc_final: 0.8615 (p) REVERT: A 316 MET cc_start: 0.9638 (mmm) cc_final: 0.9416 (tpp) REVERT: A 318 ARG cc_start: 0.9330 (mtm-85) cc_final: 0.8816 (mmp80) REVERT: A 320 LEU cc_start: 0.9642 (mt) cc_final: 0.9174 (mt) REVERT: A 653 HIS cc_start: 0.9466 (m-70) cc_final: 0.9093 (m90) REVERT: A 658 VAL cc_start: 0.9397 (p) cc_final: 0.9003 (p) REVERT: A 741 PHE cc_start: 0.9007 (m-80) cc_final: 0.8750 (m-80) REVERT: B 288 TYR cc_start: 0.9241 (m-80) cc_final: 0.8765 (m-80) REVERT: B 399 MET cc_start: 0.9251 (mmp) cc_final: 0.9048 (mmp) REVERT: B 519 PHE cc_start: 0.9524 (m-80) cc_final: 0.9138 (m-80) REVERT: B 521 MET cc_start: 0.9623 (mtm) cc_final: 0.9199 (mtp) REVERT: B 564 MET cc_start: 0.9270 (ttp) cc_final: 0.8967 (ppp) REVERT: B 584 ASN cc_start: 0.8188 (t0) cc_final: 0.7763 (m110) REVERT: B 630 HIS cc_start: 0.8744 (t70) cc_final: 0.8350 (t70) REVERT: B 653 HIS cc_start: 0.9587 (m90) cc_final: 0.9361 (m-70) REVERT: B 691 GLU cc_start: 0.9326 (tm-30) cc_final: 0.9074 (tm-30) REVERT: B 693 LEU cc_start: 0.9681 (mp) cc_final: 0.8723 (mp) REVERT: B 740 PHE cc_start: 0.9039 (t80) cc_final: 0.8783 (t80) REVERT: B 1185 MET cc_start: 0.9221 (mtt) cc_final: 0.8986 (mmt) REVERT: C 266 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8511 (tm-30) REVERT: C 320 LEU cc_start: 0.8716 (mt) cc_final: 0.8145 (mt) REVERT: C 334 TYR cc_start: 0.8545 (m-80) cc_final: 0.8014 (m-80) REVERT: C 356 LEU cc_start: 0.9593 (mt) cc_final: 0.9351 (mt) REVERT: C 399 MET cc_start: 0.9462 (mmp) cc_final: 0.8279 (tmm) REVERT: C 415 ASN cc_start: 0.9622 (p0) cc_final: 0.8623 (t0) REVERT: C 441 ARG cc_start: 0.9083 (tpp80) cc_final: 0.8854 (tpp80) REVERT: C 442 ASP cc_start: 0.9512 (p0) cc_final: 0.9073 (p0) REVERT: C 480 ARG cc_start: 0.9593 (mmt90) cc_final: 0.9047 (mmm-85) REVERT: C 521 MET cc_start: 0.9563 (mtm) cc_final: 0.9227 (mtp) REVERT: C 592 LEU cc_start: 0.9303 (pt) cc_final: 0.8827 (pt) REVERT: C 1152 HIS cc_start: 0.9327 (m170) cc_final: 0.8717 (m-70) REVERT: D 370 PHE cc_start: 0.8779 (m-80) cc_final: 0.8542 (m-80) REVERT: D 591 ARG cc_start: 0.9280 (mtt90) cc_final: 0.9012 (mtt-85) REVERT: D 636 MET cc_start: 0.9660 (pmm) cc_final: 0.9431 (pmm) REVERT: E 316 MET cc_start: 0.9467 (mmt) cc_final: 0.8614 (tpp) REVERT: E 320 LEU cc_start: 0.9651 (mt) cc_final: 0.9079 (mt) REVERT: E 335 MET cc_start: 0.9450 (mmp) cc_final: 0.9045 (mmp) REVERT: E 479 LEU cc_start: 0.9473 (mt) cc_final: 0.9225 (mt) REVERT: E 591 ARG cc_start: 0.8683 (mtt90) cc_final: 0.7968 (mmp80) REVERT: E 592 LEU cc_start: 0.9390 (pt) cc_final: 0.9024 (pt) REVERT: E 636 MET cc_start: 0.9577 (mpp) cc_final: 0.9345 (mmt) REVERT: E 641 GLN cc_start: 0.9460 (pp30) cc_final: 0.9205 (pp30) REVERT: E 642 ASP cc_start: 0.8973 (t0) cc_final: 0.8721 (t70) REVERT: E 653 HIS cc_start: 0.9781 (m-70) cc_final: 0.9510 (m-70) REVERT: E 697 ASP cc_start: 0.9379 (t0) cc_final: 0.9057 (t0) REVERT: E 701 PHE cc_start: 0.9502 (t80) cc_final: 0.8603 (t80) REVERT: F 297 MET cc_start: 0.9301 (ptt) cc_final: 0.8793 (mmm) REVERT: F 303 VAL cc_start: 0.9358 (t) cc_final: 0.9061 (t) REVERT: F 328 ASN cc_start: 0.8113 (t0) cc_final: 0.7799 (m-40) REVERT: F 370 PHE cc_start: 0.9099 (m-80) cc_final: 0.8634 (m-80) REVERT: F 432 ARG cc_start: 0.8886 (mmt180) cc_final: 0.8656 (mpp-170) REVERT: F 451 HIS cc_start: 0.8951 (m90) cc_final: 0.8517 (m-70) REVERT: F 456 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7635 (p0) REVERT: F 523 MET cc_start: 0.8172 (mmp) cc_final: 0.7937 (mmm) REVERT: F 584 ASN cc_start: 0.8397 (t0) cc_final: 0.7953 (p0) REVERT: F 593 GLU cc_start: 0.9597 (pp20) cc_final: 0.9352 (pp20) REVERT: F 622 ILE cc_start: 0.9063 (pt) cc_final: 0.8823 (pt) REVERT: F 673 ASN cc_start: 0.9368 (t0) cc_final: 0.9110 (m-40) REVERT: F 674 TRP cc_start: 0.9402 (t60) cc_final: 0.9157 (t60) REVERT: F 689 MET cc_start: 0.9689 (mmm) cc_final: 0.9296 (mmm) REVERT: F 727 TYR cc_start: 0.8393 (t80) cc_final: 0.8101 (t80) REVERT: F 741 PHE cc_start: 0.9218 (m-80) cc_final: 0.8770 (m-10) outliers start: 7 outliers final: 0 residues processed: 594 average time/residue: 0.2204 time to fit residues: 196.1032 Evaluate side-chains 436 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 435 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 145 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 293 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 199 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 329 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 661 HIS B 415 ASN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 HIS D 724 GLN E 489 ASN E 506 GLN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F1154 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.086021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.060341 restraints weight = 169419.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.061596 restraints weight = 132961.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.062471 restraints weight = 110631.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063293 restraints weight = 95939.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.063756 restraints weight = 86080.709| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28404 Z= 0.135 Angle : 0.678 9.534 38466 Z= 0.347 Chirality : 0.046 0.231 4302 Planarity : 0.006 0.075 4950 Dihedral : 6.064 41.520 3762 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.35 % Allowed : 3.83 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.14), residues: 3438 helix: -1.03 (0.12), residues: 1650 sheet: -1.19 (0.26), residues: 402 loop : -3.03 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 659 TYR 0.018 0.001 TYR F1158 PHE 0.036 0.002 PHE C 357 TRP 0.018 0.001 TRP E 674 HIS 0.009 0.001 HIS D 661 Details of bonding type rmsd covalent geometry : bond 0.00290 (28404) covalent geometry : angle 0.67828 (38466) hydrogen bonds : bond 0.03520 ( 1115) hydrogen bonds : angle 4.80942 ( 3306) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 577 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 LEU cc_start: 0.9647 (mt) cc_final: 0.9427 (mt) REVERT: A 371 ASP cc_start: 0.9569 (t0) cc_final: 0.9259 (m-30) REVERT: A 653 HIS cc_start: 0.9486 (m-70) cc_final: 0.9156 (m-70) REVERT: A 741 PHE cc_start: 0.9050 (m-80) cc_final: 0.8750 (m-80) REVERT: A 1152 HIS cc_start: 0.9781 (m90) cc_final: 0.9320 (m-70) REVERT: B 288 TYR cc_start: 0.9254 (m-80) cc_final: 0.8860 (m-80) REVERT: B 405 ARG cc_start: 0.8278 (ptt180) cc_final: 0.7713 (mtm110) REVERT: B 519 PHE cc_start: 0.9530 (m-80) cc_final: 0.9171 (m-80) REVERT: B 521 MET cc_start: 0.9584 (mtm) cc_final: 0.9119 (mtp) REVERT: B 564 MET cc_start: 0.9247 (ttp) cc_final: 0.8857 (tmm) REVERT: B 584 ASN cc_start: 0.8391 (t0) cc_final: 0.7995 (m110) REVERT: B 595 PHE cc_start: 0.9322 (m-80) cc_final: 0.9090 (m-10) REVERT: B 653 HIS cc_start: 0.9597 (m90) cc_final: 0.9366 (m-70) REVERT: B 658 VAL cc_start: 0.9444 (m) cc_final: 0.9178 (m) REVERT: B 660 ARG cc_start: 0.8788 (mmt180) cc_final: 0.8489 (mmt180) REVERT: B 691 GLU cc_start: 0.9400 (tm-30) cc_final: 0.9152 (tm-30) REVERT: B 1185 MET cc_start: 0.9095 (mtt) cc_final: 0.8868 (mmt) REVERT: C 266 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8490 (tm-30) REVERT: C 320 LEU cc_start: 0.8701 (mt) cc_final: 0.8126 (mt) REVERT: C 334 TYR cc_start: 0.8481 (m-80) cc_final: 0.7973 (m-80) REVERT: C 356 LEU cc_start: 0.9530 (mt) cc_final: 0.9193 (mt) REVERT: C 399 MET cc_start: 0.9386 (mmp) cc_final: 0.8383 (ttm) REVERT: C 402 MET cc_start: 0.9337 (tmm) cc_final: 0.9135 (ppp) REVERT: C 442 ASP cc_start: 0.9570 (p0) cc_final: 0.9148 (p0) REVERT: C 480 ARG cc_start: 0.9599 (mmt90) cc_final: 0.9078 (mmm-85) REVERT: C 521 MET cc_start: 0.9537 (mtm) cc_final: 0.9171 (mtp) REVERT: C 592 LEU cc_start: 0.9298 (pt) cc_final: 0.8859 (pt) REVERT: C 636 MET cc_start: 0.9223 (pmm) cc_final: 0.8930 (pmm) REVERT: C 1152 HIS cc_start: 0.9286 (m170) cc_final: 0.9064 (m-70) REVERT: D 277 GLN cc_start: 0.9174 (tp40) cc_final: 0.8876 (tp40) REVERT: D 370 PHE cc_start: 0.8837 (m-80) cc_final: 0.8450 (m-80) REVERT: E 328 ASN cc_start: 0.8733 (t0) cc_final: 0.8313 (p0) REVERT: E 592 LEU cc_start: 0.9403 (pt) cc_final: 0.9084 (pt) REVERT: E 636 MET cc_start: 0.9583 (mpp) cc_final: 0.9213 (mmt) REVERT: E 641 GLN cc_start: 0.9413 (pp30) cc_final: 0.9115 (pt0) REVERT: E 642 ASP cc_start: 0.8959 (t0) cc_final: 0.8072 (t70) REVERT: E 689 MET cc_start: 0.9186 (ttp) cc_final: 0.8911 (ttp) REVERT: E 697 ASP cc_start: 0.9333 (t0) cc_final: 0.8995 (t0) REVERT: E 701 PHE cc_start: 0.9509 (t80) cc_final: 0.8746 (t80) REVERT: F 303 VAL cc_start: 0.9325 (t) cc_final: 0.8970 (t) REVERT: F 328 ASN cc_start: 0.8180 (t0) cc_final: 0.7880 (m-40) REVERT: F 358 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8807 (mm-30) REVERT: F 370 PHE cc_start: 0.9098 (m-80) cc_final: 0.8782 (m-80) REVERT: F 402 MET cc_start: 0.7436 (mtt) cc_final: 0.7018 (mtt) REVERT: F 432 ARG cc_start: 0.8846 (mmt180) cc_final: 0.8615 (mpp-170) REVERT: F 451 HIS cc_start: 0.8886 (m90) cc_final: 0.8520 (m-70) REVERT: F 584 ASN cc_start: 0.8483 (t0) cc_final: 0.7984 (p0) REVERT: F 622 ILE cc_start: 0.9091 (pt) cc_final: 0.8862 (pt) REVERT: F 656 LEU cc_start: 0.9722 (tt) cc_final: 0.9382 (tt) REVERT: F 673 ASN cc_start: 0.9423 (t0) cc_final: 0.9165 (m-40) REVERT: F 674 TRP cc_start: 0.9418 (t60) cc_final: 0.9018 (t60) REVERT: F 689 MET cc_start: 0.9708 (mmm) cc_final: 0.9324 (mmm) REVERT: F 727 TYR cc_start: 0.8436 (t80) cc_final: 0.8128 (t80) REVERT: F 741 PHE cc_start: 0.9213 (m-80) cc_final: 0.8709 (m-10) REVERT: F 1154 HIS cc_start: 0.9245 (t70) cc_final: 0.8337 (t-90) REVERT: F 1158 TYR cc_start: 0.9364 (m-10) cc_final: 0.9100 (m-10) outliers start: 11 outliers final: 2 residues processed: 585 average time/residue: 0.2111 time to fit residues: 186.8000 Evaluate side-chains 426 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 424 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 149 optimal weight: 20.0000 chunk 254 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 285 optimal weight: 40.0000 chunk 10 optimal weight: 7.9990 chunk 238 optimal weight: 8.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 HIS ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN ** E 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 615 GLN ** F 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.076366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.051702 restraints weight = 178991.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.052839 restraints weight = 141848.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.053495 restraints weight = 117894.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054255 restraints weight = 103436.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.054595 restraints weight = 93512.861| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 28404 Z= 0.261 Angle : 0.836 10.615 38466 Z= 0.437 Chirality : 0.050 0.227 4302 Planarity : 0.007 0.072 4950 Dihedral : 6.430 41.816 3762 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 30.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.13), residues: 3438 helix: -1.26 (0.12), residues: 1620 sheet: -1.23 (0.26), residues: 372 loop : -2.96 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 660 TYR 0.030 0.002 TYR F 601 PHE 0.032 0.003 PHE B 305 TRP 0.020 0.002 TRP B1162 HIS 0.013 0.003 HIS D 630 Details of bonding type rmsd covalent geometry : bond 0.00528 (28404) covalent geometry : angle 0.83631 (38466) hydrogen bonds : bond 0.04243 ( 1115) hydrogen bonds : angle 5.35737 ( 3306) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 525 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 THR cc_start: 0.9224 (p) cc_final: 0.8735 (p) REVERT: A 316 MET cc_start: 0.9679 (tpt) cc_final: 0.9361 (tpp) REVERT: A 318 ARG cc_start: 0.9376 (mtm110) cc_final: 0.8876 (mmp80) REVERT: A 527 ILE cc_start: 0.9556 (tp) cc_final: 0.9336 (tp) REVERT: A 640 LEU cc_start: 0.9678 (mm) cc_final: 0.8993 (tp) REVERT: A 653 HIS cc_start: 0.9478 (m-70) cc_final: 0.9133 (m-70) REVERT: A 673 ASN cc_start: 0.9492 (t0) cc_final: 0.9281 (t0) REVERT: A 741 PHE cc_start: 0.9204 (m-80) cc_final: 0.8962 (m-80) REVERT: B 305 PHE cc_start: 0.9460 (m-10) cc_final: 0.8832 (m-80) REVERT: B 469 GLU cc_start: 0.9677 (pt0) cc_final: 0.9473 (pt0) REVERT: B 519 PHE cc_start: 0.9545 (m-80) cc_final: 0.9203 (m-80) REVERT: B 521 MET cc_start: 0.9587 (mtm) cc_final: 0.9122 (mtm) REVERT: B 564 MET cc_start: 0.9243 (ttp) cc_final: 0.8916 (ppp) REVERT: B 595 PHE cc_start: 0.9263 (m-80) cc_final: 0.9049 (m-10) REVERT: B 653 HIS cc_start: 0.9571 (m90) cc_final: 0.9268 (m-70) REVERT: B 691 GLU cc_start: 0.9495 (tm-30) cc_final: 0.9234 (tm-30) REVERT: B 740 PHE cc_start: 0.9202 (t80) cc_final: 0.8973 (t80) REVERT: C 266 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8413 (tm-30) REVERT: C 320 LEU cc_start: 0.8794 (mt) cc_final: 0.8251 (mt) REVERT: C 334 TYR cc_start: 0.8543 (m-80) cc_final: 0.8105 (m-80) REVERT: C 402 MET cc_start: 0.9364 (tmm) cc_final: 0.9111 (ppp) REVERT: C 519 PHE cc_start: 0.9481 (m-80) cc_final: 0.9164 (m-80) REVERT: C 521 MET cc_start: 0.9519 (mtm) cc_final: 0.9179 (mtp) REVERT: C 592 LEU cc_start: 0.9480 (pt) cc_final: 0.9130 (pt) REVERT: C 1152 HIS cc_start: 0.9301 (m170) cc_final: 0.8739 (m-70) REVERT: C 1158 TYR cc_start: 0.9630 (m-10) cc_final: 0.9322 (m-80) REVERT: D 277 GLN cc_start: 0.9204 (tp40) cc_final: 0.8946 (tp-100) REVERT: D 281 MET cc_start: 0.6696 (mpp) cc_final: 0.6416 (mpp) REVERT: D 370 PHE cc_start: 0.8986 (m-80) cc_final: 0.8647 (m-80) REVERT: D 371 ASP cc_start: 0.9630 (m-30) cc_final: 0.9334 (p0) REVERT: D 451 HIS cc_start: 0.9115 (m170) cc_final: 0.8761 (m-70) REVERT: D 591 ARG cc_start: 0.9291 (mtt90) cc_final: 0.9047 (mtt-85) REVERT: D 636 MET cc_start: 0.9741 (pmm) cc_final: 0.9487 (pmm) REVERT: D 692 ARG cc_start: 0.9788 (tpm170) cc_final: 0.9570 (tpp80) REVERT: E 371 ASP cc_start: 0.9141 (t70) cc_final: 0.8807 (p0) REVERT: E 592 LEU cc_start: 0.9427 (pt) cc_final: 0.9132 (pt) REVERT: E 636 MET cc_start: 0.9457 (mpp) cc_final: 0.8657 (mmm) REVERT: E 639 LEU cc_start: 0.9797 (mt) cc_final: 0.9584 (mt) REVERT: E 641 GLN cc_start: 0.9374 (pp30) cc_final: 0.9151 (pp30) REVERT: E 642 ASP cc_start: 0.9038 (t0) cc_final: 0.8723 (t70) REVERT: E 650 SER cc_start: 0.9765 (p) cc_final: 0.9527 (p) REVERT: E 674 TRP cc_start: 0.8945 (t60) cc_final: 0.8571 (t-100) REVERT: E 697 ASP cc_start: 0.9339 (t0) cc_final: 0.9065 (t0) REVERT: E 701 PHE cc_start: 0.9669 (t80) cc_final: 0.8896 (t80) REVERT: F 297 MET cc_start: 0.9273 (ptt) cc_final: 0.8735 (mmm) REVERT: F 303 VAL cc_start: 0.9411 (t) cc_final: 0.8992 (t) REVERT: F 357 PHE cc_start: 0.9583 (m-10) cc_final: 0.9373 (m-10) REVERT: F 402 MET cc_start: 0.7545 (mtt) cc_final: 0.7246 (mtt) REVERT: F 415 ASN cc_start: 0.8830 (p0) cc_final: 0.8581 (m-40) REVERT: F 432 ARG cc_start: 0.8863 (mmt180) cc_final: 0.8643 (mtm-85) REVERT: F 451 HIS cc_start: 0.8986 (m90) cc_final: 0.8611 (m-70) REVERT: F 674 TRP cc_start: 0.9514 (t60) cc_final: 0.9305 (t60) REVERT: F 689 MET cc_start: 0.9764 (mmm) cc_final: 0.9369 (mmm) REVERT: F 741 PHE cc_start: 0.9300 (m-80) cc_final: 0.8808 (m-10) REVERT: F 1154 HIS cc_start: 0.9248 (t70) cc_final: 0.8475 (t70) REVERT: F 1158 TYR cc_start: 0.9427 (m-10) cc_final: 0.9021 (m-80) outliers start: 3 outliers final: 1 residues processed: 527 average time/residue: 0.2010 time to fit residues: 162.3416 Evaluate side-chains 393 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 291 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 299 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN C 489 ASN C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 653 HIS ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.080681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.056010 restraints weight = 185384.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.057172 restraints weight = 142091.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.058169 restraints weight = 116422.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.058707 restraints weight = 100624.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059273 restraints weight = 91519.834| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28404 Z= 0.173 Angle : 0.730 9.569 38466 Z= 0.374 Chirality : 0.048 0.225 4302 Planarity : 0.006 0.071 4950 Dihedral : 6.180 41.945 3762 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.14), residues: 3438 helix: -0.98 (0.12), residues: 1620 sheet: -1.36 (0.26), residues: 402 loop : -2.75 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 354 TYR 0.027 0.002 TYR F 601 PHE 0.019 0.002 PHE F 701 TRP 0.023 0.002 TRP A 674 HIS 0.010 0.002 HIS E1154 Details of bonding type rmsd covalent geometry : bond 0.00371 (28404) covalent geometry : angle 0.73014 (38466) hydrogen bonds : bond 0.03754 ( 1115) hydrogen bonds : angle 5.01008 ( 3306) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 THR cc_start: 0.9182 (p) cc_final: 0.8662 (p) REVERT: A 316 MET cc_start: 0.9689 (tpt) cc_final: 0.9331 (tpp) REVERT: A 318 ARG cc_start: 0.9272 (mtm110) cc_final: 0.8700 (mmp80) REVERT: A 320 LEU cc_start: 0.9676 (mt) cc_final: 0.9450 (mt) REVERT: A 334 TYR cc_start: 0.8006 (m-80) cc_final: 0.7788 (m-80) REVERT: A 653 HIS cc_start: 0.9504 (m-70) cc_final: 0.9178 (m-70) REVERT: A 657 GLU cc_start: 0.9571 (mp0) cc_final: 0.9340 (mp0) REVERT: A 689 MET cc_start: 0.9609 (mmm) cc_final: 0.9271 (mmm) REVERT: A 697 ASP cc_start: 0.8749 (m-30) cc_final: 0.8449 (m-30) REVERT: A 741 PHE cc_start: 0.9114 (m-80) cc_final: 0.8855 (m-80) REVERT: A 1152 HIS cc_start: 0.9772 (m90) cc_final: 0.9321 (m-70) REVERT: B 305 PHE cc_start: 0.9446 (m-10) cc_final: 0.8822 (m-80) REVERT: B 411 ILE cc_start: 0.9644 (mp) cc_final: 0.9400 (mp) REVERT: B 469 GLU cc_start: 0.9665 (pt0) cc_final: 0.9448 (pt0) REVERT: B 519 PHE cc_start: 0.9522 (m-80) cc_final: 0.9188 (m-80) REVERT: B 521 MET cc_start: 0.9611 (mtm) cc_final: 0.9156 (mtp) REVERT: B 564 MET cc_start: 0.9203 (ttp) cc_final: 0.8911 (ppp) REVERT: B 595 PHE cc_start: 0.9325 (m-80) cc_final: 0.9065 (m-10) REVERT: B 630 HIS cc_start: 0.9611 (t70) cc_final: 0.9170 (t70) REVERT: B 653 HIS cc_start: 0.9587 (m90) cc_final: 0.9251 (m-70) REVERT: B 691 GLU cc_start: 0.9515 (tm-30) cc_final: 0.9306 (tm-30) REVERT: B 1185 MET cc_start: 0.9026 (mtt) cc_final: 0.8644 (mmm) REVERT: C 266 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8484 (tm-30) REVERT: C 320 LEU cc_start: 0.8748 (mt) cc_final: 0.8131 (mt) REVERT: C 334 TYR cc_start: 0.8484 (m-80) cc_final: 0.8012 (m-80) REVERT: C 402 MET cc_start: 0.9364 (tmm) cc_final: 0.9152 (ppp) REVERT: C 480 ARG cc_start: 0.9660 (mmt90) cc_final: 0.9125 (mmm-85) REVERT: C 519 PHE cc_start: 0.9436 (m-80) cc_final: 0.9117 (m-80) REVERT: C 521 MET cc_start: 0.9512 (mtm) cc_final: 0.9120 (mtp) REVERT: C 592 LEU cc_start: 0.9528 (pt) cc_final: 0.9164 (pt) REVERT: C 636 MET cc_start: 0.9330 (pmm) cc_final: 0.8892 (pmm) REVERT: C 689 MET cc_start: 0.9502 (mmp) cc_final: 0.9292 (mmm) REVERT: D 277 GLN cc_start: 0.9198 (tp40) cc_final: 0.8924 (tp40) REVERT: D 281 MET cc_start: 0.6667 (mpp) cc_final: 0.6301 (mpp) REVERT: D 316 MET cc_start: 0.9219 (mmp) cc_final: 0.9005 (mmm) REVERT: D 320 LEU cc_start: 0.9531 (tp) cc_final: 0.9327 (mt) REVERT: D 355 LEU cc_start: 0.9783 (mm) cc_final: 0.9554 (mm) REVERT: D 370 PHE cc_start: 0.9134 (m-80) cc_final: 0.8873 (m-80) REVERT: D 371 ASP cc_start: 0.9601 (m-30) cc_final: 0.9330 (p0) REVERT: D 692 ARG cc_start: 0.9781 (tpm170) cc_final: 0.9529 (tpp80) REVERT: E 316 MET cc_start: 0.9249 (mtt) cc_final: 0.9043 (mtt) REVERT: E 328 ASN cc_start: 0.8677 (t0) cc_final: 0.8237 (p0) REVERT: E 371 ASP cc_start: 0.9212 (t70) cc_final: 0.8891 (p0) REVERT: E 592 LEU cc_start: 0.9438 (pt) cc_final: 0.9143 (pt) REVERT: E 636 MET cc_start: 0.9571 (mpp) cc_final: 0.9087 (mpp) REVERT: E 642 ASP cc_start: 0.9038 (t0) cc_final: 0.8616 (t70) REVERT: E 666 ILE cc_start: 0.9098 (mm) cc_final: 0.8655 (mm) REVERT: E 674 TRP cc_start: 0.8875 (t60) cc_final: 0.8566 (t60) REVERT: E 697 ASP cc_start: 0.9358 (t0) cc_final: 0.9077 (t0) REVERT: E 701 PHE cc_start: 0.9692 (t80) cc_final: 0.8951 (t80) REVERT: E 741 PHE cc_start: 0.9476 (m-80) cc_final: 0.9245 (m-80) REVERT: F 402 MET cc_start: 0.7343 (mtt) cc_final: 0.7001 (mtt) REVERT: F 451 HIS cc_start: 0.8806 (m90) cc_final: 0.8402 (m-70) REVERT: F 527 ILE cc_start: 0.7649 (mp) cc_final: 0.7317 (tt) REVERT: F 656 LEU cc_start: 0.9797 (tt) cc_final: 0.9516 (tt) REVERT: F 689 MET cc_start: 0.9763 (mmm) cc_final: 0.9354 (mmm) REVERT: F 701 PHE cc_start: 0.9495 (t80) cc_final: 0.8427 (t80) REVERT: F 741 PHE cc_start: 0.9207 (m-80) cc_final: 0.8677 (m-10) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.1978 time to fit residues: 156.8270 Evaluate side-chains 387 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 192 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 266 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 331 optimal weight: 0.3980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 506 GLN C 364 GLN C 489 ASN C 506 GLN C1152 HIS ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 ASN E 506 GLN ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 HIS ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 489 ASN F 506 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.082641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.057763 restraints weight = 172021.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.059023 restraints weight = 131516.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.059979 restraints weight = 107745.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.060676 restraints weight = 92491.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.061113 restraints weight = 82592.322| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.6166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28404 Z= 0.127 Angle : 0.712 15.795 38466 Z= 0.359 Chirality : 0.047 0.253 4302 Planarity : 0.006 0.069 4950 Dihedral : 5.862 41.413 3762 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.14), residues: 3438 helix: -0.75 (0.13), residues: 1626 sheet: -1.22 (0.26), residues: 402 loop : -2.75 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 441 TYR 0.032 0.002 TYR F1158 PHE 0.030 0.001 PHE C 357 TRP 0.033 0.001 TRP F 674 HIS 0.010 0.001 HIS B1154 Details of bonding type rmsd covalent geometry : bond 0.00275 (28404) covalent geometry : angle 0.71181 (38466) hydrogen bonds : bond 0.03583 ( 1115) hydrogen bonds : angle 4.90253 ( 3306) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 THR cc_start: 0.9078 (p) cc_final: 0.8502 (p) REVERT: A 316 MET cc_start: 0.9699 (tpt) cc_final: 0.9299 (tpp) REVERT: A 318 ARG cc_start: 0.9205 (mtm110) cc_final: 0.8657 (mmp80) REVERT: A 320 LEU cc_start: 0.9659 (mt) cc_final: 0.9449 (mt) REVERT: A 334 TYR cc_start: 0.8143 (m-80) cc_final: 0.7837 (m-80) REVERT: A 371 ASP cc_start: 0.9709 (t0) cc_final: 0.9452 (m-30) REVERT: A 653 HIS cc_start: 0.9532 (m-70) cc_final: 0.9208 (m-70) REVERT: A 657 GLU cc_start: 0.9509 (mp0) cc_final: 0.9282 (mp0) REVERT: A 689 MET cc_start: 0.9607 (mmm) cc_final: 0.8743 (mmm) REVERT: A 697 ASP cc_start: 0.8806 (m-30) cc_final: 0.8494 (m-30) REVERT: A 741 PHE cc_start: 0.9068 (m-80) cc_final: 0.8796 (m-80) REVERT: A 1152 HIS cc_start: 0.9775 (m90) cc_final: 0.9310 (m-70) REVERT: B 305 PHE cc_start: 0.9382 (m-10) cc_final: 0.8735 (m-10) REVERT: B 318 ARG cc_start: 0.9383 (tpm170) cc_final: 0.9082 (tpm170) REVERT: B 469 GLU cc_start: 0.9658 (pt0) cc_final: 0.9457 (pt0) REVERT: B 519 PHE cc_start: 0.9563 (m-80) cc_final: 0.9265 (m-80) REVERT: B 521 MET cc_start: 0.9605 (mtm) cc_final: 0.9127 (mtp) REVERT: B 595 PHE cc_start: 0.9305 (m-80) cc_final: 0.9016 (m-10) REVERT: B 630 HIS cc_start: 0.9608 (t70) cc_final: 0.9055 (t-90) REVERT: B 653 HIS cc_start: 0.9490 (m90) cc_final: 0.9216 (m-70) REVERT: B 691 GLU cc_start: 0.9495 (tm-30) cc_final: 0.9279 (tm-30) REVERT: B 740 PHE cc_start: 0.9254 (t80) cc_final: 0.9003 (t80) REVERT: B 1185 MET cc_start: 0.9140 (mtt) cc_final: 0.8694 (mmm) REVERT: C 320 LEU cc_start: 0.8691 (mt) cc_final: 0.8131 (mt) REVERT: C 334 TYR cc_start: 0.8446 (m-80) cc_final: 0.7960 (m-80) REVERT: C 480 ARG cc_start: 0.9665 (mmt90) cc_final: 0.9116 (mmm-85) REVERT: C 519 PHE cc_start: 0.9388 (m-80) cc_final: 0.9097 (m-80) REVERT: C 523 MET cc_start: 0.9532 (tpp) cc_final: 0.9192 (tpp) REVERT: C 592 LEU cc_start: 0.9599 (pt) cc_final: 0.9267 (pt) REVERT: C 636 MET cc_start: 0.9257 (pmm) cc_final: 0.8866 (pmm) REVERT: C 689 MET cc_start: 0.9472 (mmp) cc_final: 0.9197 (mmm) REVERT: D 370 PHE cc_start: 0.9192 (m-80) cc_final: 0.8847 (m-80) REVERT: D 371 ASP cc_start: 0.9582 (m-30) cc_final: 0.9294 (p0) REVERT: D 479 LEU cc_start: 0.9378 (mt) cc_final: 0.9163 (mt) REVERT: E 328 ASN cc_start: 0.8581 (t0) cc_final: 0.8089 (p0) REVERT: E 415 ASN cc_start: 0.8983 (p0) cc_final: 0.8544 (t0) REVERT: E 591 ARG cc_start: 0.8815 (mtt90) cc_final: 0.8246 (mmp80) REVERT: E 636 MET cc_start: 0.9595 (mpp) cc_final: 0.9345 (mpp) REVERT: E 653 HIS cc_start: 0.9886 (m90) cc_final: 0.9671 (m-70) REVERT: E 666 ILE cc_start: 0.8996 (mm) cc_final: 0.8558 (mm) REVERT: E 674 TRP cc_start: 0.8875 (t60) cc_final: 0.8617 (t60) REVERT: E 697 ASP cc_start: 0.9290 (t0) cc_final: 0.8939 (t0) REVERT: E 701 PHE cc_start: 0.9626 (t80) cc_final: 0.8904 (t80) REVERT: E 741 PHE cc_start: 0.9469 (m-80) cc_final: 0.9240 (m-80) REVERT: F 303 VAL cc_start: 0.9339 (t) cc_final: 0.9020 (t) REVERT: F 432 ARG cc_start: 0.8883 (mmt180) cc_final: 0.8570 (mpp-170) REVERT: F 451 HIS cc_start: 0.8782 (m90) cc_final: 0.8347 (m-70) REVERT: F 527 ILE cc_start: 0.7677 (mp) cc_final: 0.7331 (tt) REVERT: F 689 MET cc_start: 0.9721 (mmm) cc_final: 0.9339 (mmm) REVERT: F 741 PHE cc_start: 0.9144 (m-80) cc_final: 0.8581 (m-10) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.2057 time to fit residues: 169.9762 Evaluate side-chains 411 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 315 optimal weight: 10.0000 chunk 18 optimal weight: 0.2980 chunk 34 optimal weight: 9.9990 chunk 292 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 293 optimal weight: 20.0000 chunk 181 optimal weight: 3.9990 chunk 296 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 291 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN C 388 HIS C 489 ASN C 506 GLN C 589 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS C1152 HIS D 277 GLN D 388 HIS ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 661 HIS ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.078613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.054299 restraints weight = 178872.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055409 restraints weight = 136817.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.056349 restraints weight = 112385.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.056798 restraints weight = 97589.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.057439 restraints weight = 88728.850| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28404 Z= 0.179 Angle : 0.751 17.225 38466 Z= 0.383 Chirality : 0.048 0.306 4302 Planarity : 0.006 0.071 4950 Dihedral : 5.970 40.828 3762 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.14), residues: 3438 helix: -0.73 (0.13), residues: 1542 sheet: -1.30 (0.26), residues: 402 loop : -2.59 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 441 TYR 0.044 0.002 TYR B 601 PHE 0.019 0.002 PHE F 720 TRP 0.019 0.002 TRP B 674 HIS 0.010 0.002 HIS B1154 Details of bonding type rmsd covalent geometry : bond 0.00379 (28404) covalent geometry : angle 0.75122 (38466) hydrogen bonds : bond 0.03696 ( 1115) hydrogen bonds : angle 5.04700 ( 3306) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.9693 (tpt) cc_final: 0.9382 (tpp) REVERT: A 334 TYR cc_start: 0.8026 (m-80) cc_final: 0.7806 (m-80) REVERT: A 371 ASP cc_start: 0.9714 (t0) cc_final: 0.9469 (m-30) REVERT: A 438 LEU cc_start: 0.9327 (tp) cc_final: 0.9125 (tp) REVERT: A 653 HIS cc_start: 0.9511 (m-70) cc_final: 0.9174 (m-70) REVERT: A 741 PHE cc_start: 0.9066 (m-80) cc_final: 0.8848 (m-80) REVERT: A 1152 HIS cc_start: 0.9770 (m90) cc_final: 0.9306 (m-70) REVERT: B 305 PHE cc_start: 0.9475 (m-10) cc_final: 0.8767 (m-80) REVERT: B 318 ARG cc_start: 0.9424 (tpm170) cc_final: 0.9106 (tpm170) REVERT: B 411 ILE cc_start: 0.9660 (mp) cc_final: 0.9447 (mp) REVERT: B 469 GLU cc_start: 0.9693 (pt0) cc_final: 0.9490 (pt0) REVERT: B 519 PHE cc_start: 0.9516 (m-80) cc_final: 0.9210 (m-80) REVERT: B 521 MET cc_start: 0.9619 (mtm) cc_final: 0.9167 (mtp) REVERT: B 595 PHE cc_start: 0.9354 (m-80) cc_final: 0.9077 (m-10) REVERT: B 636 MET cc_start: 0.9752 (mpp) cc_final: 0.8991 (mpp) REVERT: B 658 VAL cc_start: 0.9355 (m) cc_final: 0.9115 (m) REVERT: B 740 PHE cc_start: 0.9265 (t80) cc_final: 0.9035 (t80) REVERT: C 266 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8416 (tm-30) REVERT: C 320 LEU cc_start: 0.8743 (mt) cc_final: 0.8147 (mt) REVERT: C 334 TYR cc_start: 0.8373 (m-80) cc_final: 0.7787 (m-80) REVERT: C 335 MET cc_start: 0.9137 (pmm) cc_final: 0.8846 (pmm) REVERT: C 399 MET cc_start: 0.9264 (mmp) cc_final: 0.8951 (mmt) REVERT: C 480 ARG cc_start: 0.9681 (mmt90) cc_final: 0.9175 (mmm-85) REVERT: C 519 PHE cc_start: 0.9428 (m-80) cc_final: 0.9114 (m-80) REVERT: C 521 MET cc_start: 0.9729 (mtm) cc_final: 0.9434 (mtp) REVERT: C 523 MET cc_start: 0.9450 (tpp) cc_final: 0.9143 (tpp) REVERT: C 592 LEU cc_start: 0.9589 (pt) cc_final: 0.9296 (pt) REVERT: C 689 MET cc_start: 0.9523 (mmp) cc_final: 0.9266 (mmm) REVERT: C 1152 HIS cc_start: 0.9255 (m90) cc_final: 0.8679 (m90) REVERT: D 277 GLN cc_start: 0.9116 (tp40) cc_final: 0.8826 (tp-100) REVERT: D 281 MET cc_start: 0.6574 (mpp) cc_final: 0.6083 (mpp) REVERT: D 370 PHE cc_start: 0.9192 (m-80) cc_final: 0.8880 (m-80) REVERT: D 371 ASP cc_start: 0.9622 (m-30) cc_final: 0.9379 (p0) REVERT: E 328 ASN cc_start: 0.8591 (t0) cc_final: 0.8200 (p0) REVERT: E 415 ASN cc_start: 0.9002 (p0) cc_final: 0.8507 (t0) REVERT: E 636 MET cc_start: 0.9571 (mpp) cc_final: 0.9351 (mpp) REVERT: E 666 ILE cc_start: 0.9032 (mm) cc_final: 0.8778 (mm) REVERT: E 674 TRP cc_start: 0.8923 (t60) cc_final: 0.8640 (t60) REVERT: E 689 MET cc_start: 0.9364 (ttp) cc_final: 0.9004 (ttp) REVERT: E 697 ASP cc_start: 0.9397 (t0) cc_final: 0.9062 (t70) REVERT: E 701 PHE cc_start: 0.9677 (t80) cc_final: 0.8871 (t80) REVERT: F 303 VAL cc_start: 0.9378 (t) cc_final: 0.9103 (t) REVERT: F 451 HIS cc_start: 0.8850 (m90) cc_final: 0.8360 (m-70) REVERT: F 601 TYR cc_start: 0.8274 (t80) cc_final: 0.8062 (t80) REVERT: F 656 LEU cc_start: 0.9796 (tt) cc_final: 0.9540 (tt) REVERT: F 689 MET cc_start: 0.9756 (mmm) cc_final: 0.9375 (mmm) REVERT: F 741 PHE cc_start: 0.9140 (m-80) cc_final: 0.8626 (m-10) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.2116 time to fit residues: 165.3698 Evaluate side-chains 395 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 57 optimal weight: 6.9990 chunk 285 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 340 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 329 optimal weight: 7.9990 chunk 299 optimal weight: 30.0000 chunk 117 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 506 GLN ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 HIS ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.081865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.057828 restraints weight = 196679.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.059129 restraints weight = 147835.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.060064 restraints weight = 120039.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.060770 restraints weight = 102806.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061320 restraints weight = 91243.358| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28404 Z= 0.143 Angle : 0.746 18.687 38466 Z= 0.374 Chirality : 0.048 0.322 4302 Planarity : 0.006 0.069 4950 Dihedral : 5.888 41.096 3762 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.14), residues: 3438 helix: -0.73 (0.13), residues: 1614 sheet: -1.30 (0.26), residues: 402 loop : -2.67 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 692 TYR 0.029 0.002 TYR B 601 PHE 0.026 0.002 PHE C 357 TRP 0.014 0.001 TRP A 674 HIS 0.013 0.001 HIS E 653 Details of bonding type rmsd covalent geometry : bond 0.00312 (28404) covalent geometry : angle 0.74580 (38466) hydrogen bonds : bond 0.03588 ( 1115) hydrogen bonds : angle 5.01347 ( 3306) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 THR cc_start: 0.9047 (p) cc_final: 0.8500 (p) REVERT: A 316 MET cc_start: 0.9708 (tpt) cc_final: 0.9316 (tpp) REVERT: A 318 ARG cc_start: 0.9343 (mtm110) cc_final: 0.8854 (mmp80) REVERT: A 320 LEU cc_start: 0.9689 (mt) cc_final: 0.9488 (mt) REVERT: A 371 ASP cc_start: 0.9713 (t0) cc_final: 0.9460 (m-30) REVERT: A 410 ILE cc_start: 0.8586 (pt) cc_final: 0.8354 (pt) REVERT: A 653 HIS cc_start: 0.9478 (m-70) cc_final: 0.9127 (m-70) REVERT: A 673 ASN cc_start: 0.9582 (t0) cc_final: 0.9379 (t0) REVERT: A 741 PHE cc_start: 0.9008 (m-80) cc_final: 0.8780 (m-80) REVERT: A 1152 HIS cc_start: 0.9767 (m90) cc_final: 0.9279 (m-70) REVERT: B 318 ARG cc_start: 0.9410 (tpm170) cc_final: 0.9105 (tpm170) REVERT: B 469 GLU cc_start: 0.9667 (pt0) cc_final: 0.9466 (pt0) REVERT: B 519 PHE cc_start: 0.9519 (m-80) cc_final: 0.9214 (m-80) REVERT: B 521 MET cc_start: 0.9611 (mtm) cc_final: 0.9131 (mtp) REVERT: B 595 PHE cc_start: 0.9337 (m-80) cc_final: 0.9049 (m-10) REVERT: B 740 PHE cc_start: 0.9211 (t80) cc_final: 0.9005 (t80) REVERT: B 1185 MET cc_start: 0.8912 (mtt) cc_final: 0.8632 (mmm) REVERT: C 320 LEU cc_start: 0.8709 (mt) cc_final: 0.8158 (mt) REVERT: C 334 TYR cc_start: 0.8373 (m-80) cc_final: 0.7812 (m-80) REVERT: C 335 MET cc_start: 0.9128 (pmm) cc_final: 0.8846 (pmm) REVERT: C 480 ARG cc_start: 0.9677 (mmt90) cc_final: 0.9122 (mmm-85) REVERT: C 519 PHE cc_start: 0.9407 (m-80) cc_final: 0.9091 (m-80) REVERT: C 521 MET cc_start: 0.9729 (mtm) cc_final: 0.9343 (mtp) REVERT: C 523 MET cc_start: 0.9453 (tpp) cc_final: 0.9120 (tpp) REVERT: C 592 LEU cc_start: 0.9660 (pt) cc_final: 0.9450 (pt) REVERT: C 636 MET cc_start: 0.9317 (pmm) cc_final: 0.8809 (pmm) REVERT: C 689 MET cc_start: 0.9451 (mmp) cc_final: 0.9166 (mmm) REVERT: C 1152 HIS cc_start: 0.9233 (m90) cc_final: 0.8890 (m-70) REVERT: D 277 GLN cc_start: 0.9109 (tp40) cc_final: 0.8798 (tp-100) REVERT: D 281 MET cc_start: 0.6650 (mpp) cc_final: 0.6160 (mpp) REVERT: D 370 PHE cc_start: 0.9201 (m-80) cc_final: 0.8859 (m-80) REVERT: D 371 ASP cc_start: 0.9611 (m-30) cc_final: 0.9364 (p0) REVERT: E 324 CYS cc_start: 0.9523 (t) cc_final: 0.9321 (t) REVERT: E 328 ASN cc_start: 0.8578 (t0) cc_final: 0.8239 (p0) REVERT: E 371 ASP cc_start: 0.9174 (t70) cc_final: 0.8875 (p0) REVERT: E 399 MET cc_start: 0.7892 (mmp) cc_final: 0.7609 (mmp) REVERT: E 415 ASN cc_start: 0.8897 (p0) cc_final: 0.8367 (t0) REVERT: E 666 ILE cc_start: 0.8967 (mm) cc_final: 0.8571 (mm) REVERT: E 689 MET cc_start: 0.9326 (ttp) cc_final: 0.9033 (ttt) REVERT: E 697 ASP cc_start: 0.9356 (t0) cc_final: 0.8975 (t70) REVERT: E 701 PHE cc_start: 0.9670 (t80) cc_final: 0.8930 (t80) REVERT: F 451 HIS cc_start: 0.8643 (m90) cc_final: 0.8367 (m-70) REVERT: F 527 ILE cc_start: 0.7823 (mp) cc_final: 0.7465 (tt) REVERT: F 601 TYR cc_start: 0.8265 (t80) cc_final: 0.8043 (t80) REVERT: F 645 GLN cc_start: 0.9385 (pt0) cc_final: 0.8832 (pt0) REVERT: F 653 HIS cc_start: 0.9656 (m170) cc_final: 0.9336 (m170) REVERT: F 657 GLU cc_start: 0.9719 (mp0) cc_final: 0.9474 (mp0) REVERT: F 674 TRP cc_start: 0.8954 (t60) cc_final: 0.7881 (t60) REVERT: F 675 LEU cc_start: 0.9110 (mt) cc_final: 0.8199 (mt) REVERT: F 689 MET cc_start: 0.9748 (mmm) cc_final: 0.9349 (mmm) REVERT: F 741 PHE cc_start: 0.9125 (m-80) cc_final: 0.8592 (m-10) outliers start: 0 outliers final: 0 residues processed: 525 average time/residue: 0.2046 time to fit residues: 163.6637 Evaluate side-chains 406 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 260 optimal weight: 4.9990 chunk 319 optimal weight: 10.0000 chunk 334 optimal weight: 0.4980 chunk 283 optimal weight: 5.9990 chunk 207 optimal weight: 0.0370 chunk 256 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 213 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.9064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 506 GLN ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 506 GLN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN D 661 HIS ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 HIS ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.081364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.057160 restraints weight = 189728.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.058454 restraints weight = 142272.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059410 restraints weight = 115557.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.059942 restraints weight = 98890.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060575 restraints weight = 89240.192| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.6955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28404 Z= 0.146 Angle : 0.748 10.873 38466 Z= 0.378 Chirality : 0.048 0.349 4302 Planarity : 0.006 0.069 4950 Dihedral : 5.847 40.646 3762 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.14), residues: 3438 helix: -0.63 (0.13), residues: 1566 sheet: -1.30 (0.26), residues: 402 loop : -2.70 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1179 TYR 0.030 0.002 TYR B1158 PHE 0.019 0.002 PHE F 595 TRP 0.015 0.001 TRP A 674 HIS 0.009 0.001 HIS C1154 Details of bonding type rmsd covalent geometry : bond 0.00317 (28404) covalent geometry : angle 0.74762 (38466) hydrogen bonds : bond 0.03602 ( 1115) hydrogen bonds : angle 5.05354 ( 3306) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 THR cc_start: 0.9019 (p) cc_final: 0.8474 (p) REVERT: A 316 MET cc_start: 0.9687 (tpt) cc_final: 0.9339 (tpp) REVERT: A 318 ARG cc_start: 0.9344 (mtm110) cc_final: 0.8880 (mmp80) REVERT: A 369 PHE cc_start: 0.8681 (m-10) cc_final: 0.7983 (m-80) REVERT: A 371 ASP cc_start: 0.9714 (t0) cc_final: 0.9471 (m-30) REVERT: A 653 HIS cc_start: 0.9469 (m-70) cc_final: 0.9127 (m-70) REVERT: A 741 PHE cc_start: 0.8993 (m-80) cc_final: 0.8786 (m-80) REVERT: A 1152 HIS cc_start: 0.9766 (m90) cc_final: 0.9275 (m-70) REVERT: B 316 MET cc_start: 0.8874 (tmm) cc_final: 0.8665 (tmm) REVERT: B 318 ARG cc_start: 0.9415 (tpm170) cc_final: 0.9106 (tpm170) REVERT: B 521 MET cc_start: 0.9623 (mtm) cc_final: 0.9141 (mtp) REVERT: B 595 PHE cc_start: 0.9344 (m-80) cc_final: 0.9045 (m-10) REVERT: B 1185 MET cc_start: 0.8786 (mtt) cc_final: 0.8546 (mmm) REVERT: C 320 LEU cc_start: 0.8737 (mt) cc_final: 0.8152 (mt) REVERT: C 335 MET cc_start: 0.9007 (pmm) cc_final: 0.8735 (pmm) REVERT: C 350 GLU cc_start: 0.9285 (tp30) cc_final: 0.7894 (mp0) REVERT: C 480 ARG cc_start: 0.9674 (mmt90) cc_final: 0.9123 (mmm-85) REVERT: C 519 PHE cc_start: 0.9413 (m-80) cc_final: 0.9109 (m-80) REVERT: C 521 MET cc_start: 0.9757 (mtm) cc_final: 0.9376 (mtp) REVERT: C 523 MET cc_start: 0.9463 (tpp) cc_final: 0.9132 (tpp) REVERT: C 592 LEU cc_start: 0.9678 (pt) cc_final: 0.9409 (pt) REVERT: C 689 MET cc_start: 0.9458 (mmp) cc_final: 0.9170 (mmm) REVERT: C 1152 HIS cc_start: 0.9312 (m90) cc_final: 0.8945 (m-70) REVERT: D 277 GLN cc_start: 0.9116 (tp40) cc_final: 0.8805 (tp-100) REVERT: D 281 MET cc_start: 0.6711 (mpp) cc_final: 0.6210 (mpp) REVERT: D 370 PHE cc_start: 0.9223 (m-80) cc_final: 0.8883 (m-80) REVERT: D 371 ASP cc_start: 0.9581 (m-30) cc_final: 0.9324 (p0) REVERT: D 689 MET cc_start: 0.9629 (mmp) cc_final: 0.9421 (mmm) REVERT: E 316 MET cc_start: 0.9247 (mtm) cc_final: 0.8435 (tpp) REVERT: E 320 LEU cc_start: 0.9593 (mt) cc_final: 0.9313 (mt) REVERT: E 324 CYS cc_start: 0.9516 (t) cc_final: 0.9306 (t) REVERT: E 328 ASN cc_start: 0.8527 (t0) cc_final: 0.8186 (p0) REVERT: E 415 ASN cc_start: 0.8809 (p0) cc_final: 0.8097 (t0) REVERT: E 666 ILE cc_start: 0.8971 (mm) cc_final: 0.8583 (mm) REVERT: E 689 MET cc_start: 0.9309 (ttp) cc_final: 0.9028 (ttt) REVERT: E 697 ASP cc_start: 0.9304 (t0) cc_final: 0.8922 (t70) REVERT: E 701 PHE cc_start: 0.9668 (t80) cc_final: 0.8925 (t80) REVERT: F 451 HIS cc_start: 0.8726 (m90) cc_final: 0.8259 (m-70) REVERT: F 527 ILE cc_start: 0.7827 (mp) cc_final: 0.7519 (tt) REVERT: F 601 TYR cc_start: 0.8319 (t80) cc_final: 0.8010 (t80) REVERT: F 645 GLN cc_start: 0.9382 (pt0) cc_final: 0.9068 (pt0) REVERT: F 653 HIS cc_start: 0.9669 (m170) cc_final: 0.9386 (m170) REVERT: F 656 LEU cc_start: 0.9793 (tt) cc_final: 0.9448 (tt) REVERT: F 671 ILE cc_start: 0.9815 (mp) cc_final: 0.9573 (mp) REVERT: F 674 TRP cc_start: 0.8877 (t60) cc_final: 0.7737 (t60) REVERT: F 675 LEU cc_start: 0.9137 (mt) cc_final: 0.8272 (mt) REVERT: F 689 MET cc_start: 0.9747 (mmm) cc_final: 0.9381 (mmm) REVERT: F 741 PHE cc_start: 0.9097 (m-80) cc_final: 0.8516 (m-10) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.2040 time to fit residues: 160.7474 Evaluate side-chains 403 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 201 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 295 optimal weight: 6.9990 chunk 262 optimal weight: 0.0470 chunk 28 optimal weight: 9.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 506 GLN ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 506 GLN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 661 HIS ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 HIS F 306 HIS ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN ** F 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 661 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.083163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.058605 restraints weight = 184975.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.059944 restraints weight = 138863.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.060916 restraints weight = 112784.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.061674 restraints weight = 96510.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.062061 restraints weight = 85522.591| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28404 Z= 0.126 Angle : 0.740 10.258 38466 Z= 0.371 Chirality : 0.048 0.256 4302 Planarity : 0.006 0.069 4950 Dihedral : 5.660 40.630 3762 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.14), residues: 3438 helix: -0.51 (0.13), residues: 1590 sheet: -1.18 (0.26), residues: 402 loop : -2.55 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 354 TYR 0.030 0.001 TYR B1158 PHE 0.020 0.001 PHE B 305 TRP 0.010 0.001 TRP E 674 HIS 0.020 0.002 HIS E 653 Details of bonding type rmsd covalent geometry : bond 0.00271 (28404) covalent geometry : angle 0.73988 (38466) hydrogen bonds : bond 0.03605 ( 1115) hydrogen bonds : angle 4.91190 ( 3306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5827.28 seconds wall clock time: 101 minutes 30.05 seconds (6090.05 seconds total)