Starting phenix.real_space_refine on Tue Jun 24 02:17:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jpq_9870/06_2025/6jpq_9870.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jpq_9870/06_2025/6jpq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6jpq_9870/06_2025/6jpq_9870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jpq_9870/06_2025/6jpq_9870.map" model { file = "/net/cci-nas-00/data/ceres_data/6jpq_9870/06_2025/6jpq_9870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jpq_9870/06_2025/6jpq_9870.cif" } resolution = 4.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.034 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, F Time building chain proxies: 11.09, per 1000 atoms: 0.40 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: 6.53 Conformation dependent library (CDL) restraints added in 3.9 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: 3.34 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: 10.31 Time building geometry restraints manager: 7.71 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 0.010 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 52.370 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.430 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.003 TRP E 455 HIS 0.013 0.004 HIS F 630 PHE 0.023 0.003 PHE C 436 TYR 0.024 0.004 TYR F 601 ARG 0.007 0.001 ARG C 599 Details of bonding type rmsd hydrogen bonds : bond 0.13123 ( 1115) hydrogen bonds : angle 8.93687 ( 3306) covalent geometry : bond 0.00642 (28404) covalent geometry : angle 1.13123 (38466) *********************** 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 : 3.617 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6434 (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: 0.6919 (mt) REVERT: A 640 LEU cc_start: 0.9529 (mm) cc_final: 0.9281 (mm) REVERT: A 674 TRP cc_start: 0.8525 (t60) cc_final: 0.8313 (t-100) REVERT: A 716 LEU cc_start: 0.9775 (mt) cc_final: 0.9380 (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: 0.9107 (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: 0.8962 (m-80) REVERT: A 1152 HIS cc_start: 0.9633 (m90) cc_final: 0.9361 (m-70) REVERT: B 305 PHE cc_start: 0.9684 (m-10) cc_final: 0.9333 (m-10) 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: 0.9079 (mt) REVERT: B 351 ARG cc_start: 0.9043 (ptm-80) cc_final: 0.8784 (ttp80) REVERT: B 418 ASP cc_start: 0.8693 (t0) cc_final: 0.8485 (m-30) REVERT: B 442 ASP cc_start: 0.9708 (p0) cc_final: 0.9496 (p0) REVERT: B 519 PHE cc_start: 0.9617 (m-80) cc_final: 0.9210 (m-80) REVERT: B 549 LEU cc_start: 0.9596 (mt) cc_final: 0.9251 (mp) REVERT: B 564 MET cc_start: 0.9405 (ttp) cc_final: 0.8993 (ppp) REVERT: B 584 ASN cc_start: 0.8133 (t0) cc_final: 0.7845 (m-40) REVERT: B 630 HIS cc_start: 0.8006 (t-90) cc_final: 0.7704 (t70) REVERT: B 636 MET cc_start: 0.9473 (pmm) cc_final: 0.8819 (mmt) REVERT: B 727 TYR cc_start: 0.8688 (t80) cc_final: 0.8488 (t80) REVERT: B 1185 MET cc_start: 0.9234 (mtt) cc_final: 0.8993 (mmm) REVERT: C 320 LEU cc_start: 0.8795 (mt) cc_final: 0.7943 (mt) REVERT: C 352 GLN cc_start: 0.9364 (mp10) cc_final: 0.9089 (mt0) 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: 0.9160 (mt) REVERT: D 281 MET cc_start: 0.7781 (mmt) cc_final: 0.7389 (mmm) REVERT: D 369 PHE cc_start: 0.8614 (m-10) cc_final: 0.8263 (m-80) REVERT: D 430 PHE cc_start: 0.8892 (m-10) cc_final: 0.8687 (m-80) REVERT: D 432 ARG cc_start: 0.8522 (mmt180) cc_final: 0.8320 (mtm-85) REVERT: D 636 MET cc_start: 0.9748 (pmm) cc_final: 0.9534 (pmm) REVERT: E 277 GLN cc_start: 0.9547 (mt0) cc_final: 0.9334 (mt0) 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: 0.8692 (mmt) REVERT: E 415 ASN cc_start: 0.8594 (t160) cc_final: 0.7840 (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: 0.9314 (mt) REVERT: E 591 ARG cc_start: 0.8611 (mtt90) cc_final: 0.8079 (mmp80) REVERT: E 592 LEU cc_start: 0.9338 (pt) cc_final: 0.8986 (pt) REVERT: E 653 HIS cc_start: 0.9662 (m170) cc_final: 0.9417 (m-70) REVERT: E 697 ASP cc_start: 0.9010 (m-30) cc_final: 0.8809 (t0) REVERT: E 701 PHE cc_start: 0.9281 (t80) cc_final: 0.8678 (t80) REVERT: F 277 GLN cc_start: 0.9837 (mt0) cc_final: 0.9563 (mt0) REVERT: F 298 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8336 (tp40) REVERT: F 356 LEU cc_start: 0.9661 (tt) cc_final: 0.9402 (mt) REVERT: F 432 ARG cc_start: 0.9226 (mmt180) cc_final: 0.8822 (mpp-170) REVERT: F 519 PHE cc_start: 0.9522 (m-80) cc_final: 0.9202 (t80) REVERT: F 523 MET cc_start: 0.8556 (mmm) cc_final: 0.7664 (mmp) REVERT: F 592 LEU cc_start: 0.9703 (pt) cc_final: 0.9464 (pt) REVERT: F 645 GLN cc_start: 0.8727 (pt0) cc_final: 0.8199 (pt0) REVERT: F 652 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8621 (pt) REVERT: F 653 HIS cc_start: 0.9295 (m170) cc_final: 0.8748 (m-70) REVERT: F 678 LEU cc_start: 0.8271 (mm) cc_final: 0.7787 (mm) REVERT: F 686 PHE cc_start: 0.9379 (t80) cc_final: 0.9116 (t80) REVERT: F 689 MET cc_start: 0.9615 (mmm) cc_final: 0.9312 (mmm) REVERT: F 704 LEU cc_start: 0.9359 (tp) cc_final: 0.9151 (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: 0.9267 (mm) REVERT: F 741 PHE cc_start: 0.9219 (m-80) cc_final: 0.8637 (m-80) outliers start: 18 outliers final: 2 residues processed: 812 average time/residue: 0.6060 time to fit residues: 726.3239 Evaluate side-chains 525 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 521 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 8.9990 chunk 259 optimal weight: 0.2980 chunk 143 optimal weight: 7.9990 chunk 88 optimal weight: 0.0000 chunk 174 optimal weight: 0.6980 chunk 138 optimal weight: 0.3980 chunk 268 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 310 optimal weight: 20.0000 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 497 GLN 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 506 GLN D 589 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 497 GLN E 506 GLN E 589 GLN 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.092852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065861 restraints weight = 157952.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.067186 restraints weight = 126847.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068247 restraints weight = 107021.815| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3110 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= 0.133 Angle : 0.722 10.460 38466 Z= 0.369 Chirality : 0.046 0.216 4302 Planarity : 0.007 0.108 4950 Dihedral : 6.780 44.932 3762 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.45 % Allowed : 3.58 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.13), residues: 3438 helix: -1.79 (0.12), residues: 1548 sheet: -1.16 (0.25), residues: 372 loop : -3.33 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 345 HIS 0.016 0.002 HIS F 451 PHE 0.021 0.001 PHE E 634 TYR 0.030 0.001 TYR A1158 ARG 0.011 0.001 ARG B 480 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 1115) hydrogen bonds : angle 5.31184 ( 3306) covalent geometry : bond 0.00279 (28404) covalent geometry : angle 0.72198 (38466) *********************** 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 714 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 700 time to evaluate : 2.977 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: A 283 MET cc_start: 0.9158 (ptm) cc_final: 0.8882 (ptm) REVERT: A 316 MET cc_start: 0.9566 (mmm) cc_final: 0.9272 (mmm) REVERT: A 335 MET cc_start: 0.7785 (mmt) cc_final: 0.7541 (mmp) REVERT: A 371 ASP cc_start: 0.9518 (t0) cc_final: 0.9125 (m-30) REVERT: A 402 MET cc_start: 0.7060 (mtp) cc_final: 0.6808 (mtp) REVERT: A 424 LEU cc_start: 0.8930 (mp) cc_final: 0.8344 (mp) REVERT: A 548 LEU cc_start: 0.9184 (mm) cc_final: 0.8932 (mm) REVERT: A 631 VAL cc_start: 0.9106 (t) cc_final: 0.8877 (t) REVERT: A 653 HIS cc_start: 0.9417 (m-70) cc_final: 0.9047 (m-70) REVERT: A 665 ILE cc_start: 0.9268 (mp) cc_final: 0.9004 (mp) REVERT: A 704 LEU cc_start: 0.9467 (tp) cc_final: 0.9255 (mm) REVERT: A 1152 HIS cc_start: 0.9720 (m90) cc_final: 0.9247 (m-70) REVERT: A 1157 LEU cc_start: 0.9520 (mm) cc_final: 0.9275 (pp) REVERT: B 288 TYR cc_start: 0.9328 (m-80) cc_final: 0.8995 (m-80) REVERT: B 398 LEU cc_start: 0.9540 (mp) cc_final: 0.9236 (mp) REVERT: B 399 MET cc_start: 0.9084 (mmp) cc_final: 0.8808 (mmp) REVERT: B 402 MET cc_start: 0.6338 (mtt) cc_final: 0.5936 (mtm) REVERT: B 519 PHE cc_start: 0.9634 (m-80) cc_final: 0.9311 (m-80) REVERT: B 521 MET cc_start: 0.9556 (mtm) cc_final: 0.9218 (mtp) REVERT: B 545 LEU cc_start: 0.9792 (mp) cc_final: 0.9513 (tp) REVERT: B 564 MET cc_start: 0.9287 (ttp) cc_final: 0.8925 (tmm) REVERT: B 584 ASN cc_start: 0.8832 (t0) cc_final: 0.8334 (m-40) REVERT: B 626 TYR cc_start: 0.8791 (p90) cc_final: 0.8430 (p90) REVERT: B 635 ASP cc_start: 0.9822 (t0) cc_final: 0.9598 (t0) REVERT: B 653 HIS cc_start: 0.9500 (m90) cc_final: 0.9263 (m-70) REVERT: B 660 ARG cc_start: 0.8975 (mmt180) cc_final: 0.8462 (mmt180) REVERT: B 727 TYR cc_start: 0.9057 (t80) cc_final: 0.8848 (t80) REVERT: B 1185 MET cc_start: 0.9332 (mtt) cc_final: 0.9063 (mmt) REVERT: C 266 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8495 (tm-30) REVERT: C 288 TYR cc_start: 0.9062 (m-80) cc_final: 0.8793 (m-80) REVERT: C 399 MET cc_start: 0.9431 (mmp) cc_final: 0.8377 (tmm) REVERT: C 441 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8712 (tpp80) REVERT: C 442 ASP cc_start: 0.9555 (p0) cc_final: 0.9338 (p0) REVERT: C 480 ARG cc_start: 0.9580 (mmt90) cc_final: 0.9103 (mmm-85) REVERT: C 521 MET cc_start: 0.9757 (mtm) cc_final: 0.9432 (mtm) REVERT: C 636 MET cc_start: 0.9243 (pmm) cc_final: 0.8738 (pmm) REVERT: C 670 ASP cc_start: 0.9305 (t70) cc_final: 0.9080 (p0) REVERT: C 689 MET cc_start: 0.9124 (mmp) cc_final: 0.8922 (mmm) REVERT: C 765 VAL cc_start: 0.8867 (m) cc_final: 0.8650 (p) REVERT: C 1152 HIS cc_start: 0.9390 (m170) cc_final: 0.9024 (m-70) REVERT: D 281 MET cc_start: 0.7765 (mmt) cc_final: 0.7528 (mmt) REVERT: D 283 MET cc_start: 0.8235 (ptt) cc_final: 0.7872 (ptt) REVERT: D 316 MET cc_start: 0.9269 (mmt) cc_final: 0.8922 (mmm) REVERT: D 416 ARG cc_start: 0.9005 (pmt170) cc_final: 0.8746 (pmt-80) REVERT: D 591 ARG cc_start: 0.9345 (mtt90) cc_final: 0.9107 (mtt-85) REVERT: D 692 ARG cc_start: 0.9455 (tpm170) cc_final: 0.8965 (ttp80) REVERT: D 1184 PHE cc_start: 0.8782 (t80) cc_final: 0.8171 (t80) REVERT: E 371 ASP cc_start: 0.9543 (m-30) cc_final: 0.9318 (t0) REVERT: E 479 LEU cc_start: 0.9456 (mt) cc_final: 0.9253 (mt) REVERT: E 591 ARG cc_start: 0.8609 (mtt90) cc_final: 0.8052 (mmp80) REVERT: E 592 LEU cc_start: 0.9308 (pt) cc_final: 0.8988 (pt) REVERT: E 635 ASP cc_start: 0.9663 (t70) cc_final: 0.9346 (t0) REVERT: E 642 ASP cc_start: 0.7570 (t70) cc_final: 0.7003 (t70) REVERT: E 697 ASP cc_start: 0.9210 (m-30) cc_final: 0.8520 (t0) REVERT: E 701 PHE cc_start: 0.9267 (t80) cc_final: 0.8633 (t80) REVERT: E 1179 ARG cc_start: 0.9712 (mpp-170) cc_final: 0.9344 (ptt180) REVERT: F 274 TYR cc_start: 0.9477 (m-10) cc_final: 0.9220 (m-10) REVERT: F 298 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8204 (pp30) REVERT: F 303 VAL cc_start: 0.9196 (t) cc_final: 0.8890 (t) REVERT: F 335 MET cc_start: 0.8573 (mmt) cc_final: 0.8155 (mmp) REVERT: F 351 ARG cc_start: 0.8231 (mmp80) cc_final: 0.7897 (mmp80) REVERT: F 432 ARG cc_start: 0.8957 (mmt180) cc_final: 0.8746 (mpp-170) REVERT: F 519 PHE cc_start: 0.9506 (m-80) cc_final: 0.9237 (m-80) REVERT: F 523 MET cc_start: 0.8411 (mmm) cc_final: 0.8078 (mmm) REVERT: F 584 ASN cc_start: 0.8734 (t0) cc_final: 0.8208 (p0) REVERT: F 601 TYR cc_start: 0.8002 (t80) cc_final: 0.7720 (t80) REVERT: F 622 ILE cc_start: 0.8933 (pt) cc_final: 0.8667 (pt) REVERT: F 636 MET cc_start: 0.9077 (mpp) cc_final: 0.8724 (mmt) REVERT: F 656 LEU cc_start: 0.9827 (tt) cc_final: 0.9165 (tt) REVERT: F 660 ARG cc_start: 0.9613 (mmp-170) cc_final: 0.9182 (mmm-85) REVERT: F 674 TRP cc_start: 0.9556 (t-100) cc_final: 0.9247 (t-100) REVERT: F 678 LEU cc_start: 0.8235 (mm) cc_final: 0.8003 (mm) REVERT: F 689 MET cc_start: 0.9670 (mmm) cc_final: 0.9250 (mtm) REVERT: F 697 ASP cc_start: 0.8601 (m-30) cc_final: 0.8254 (m-30) REVERT: F 720 PHE cc_start: 0.9398 (m-80) cc_final: 0.9198 (m-80) REVERT: F 727 TYR cc_start: 0.8356 (t80) cc_final: 0.8052 (t80) REVERT: F 738 ILE cc_start: 0.9654 (pt) cc_final: 0.9351 (mm) REVERT: F 741 PHE cc_start: 0.9307 (m-80) cc_final: 0.8756 (m-80) REVERT: F 754 GLU cc_start: 0.9192 (mp0) cc_final: 0.8990 (mp0) REVERT: F 1154 HIS cc_start: 0.9147 (t70) cc_final: 0.8506 (t-90) outliers start: 14 outliers final: 1 residues processed: 709 average time/residue: 0.4762 time to fit residues: 500.0703 Evaluate side-chains 522 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 521 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 209 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 315 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 326 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 497 GLN A 506 GLN A 589 GLN A 661 HIS ** A1154 HIS ** 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 ** 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 ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN ** D 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1136 GLN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 653 HIS E 661 HIS ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 661 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.085379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060249 restraints weight = 183794.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.061452 restraints weight = 143996.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.062485 restraints weight = 118923.762| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28404 Z= 0.195 Angle : 0.752 9.741 38466 Z= 0.392 Chirality : 0.047 0.213 4302 Planarity : 0.007 0.079 4950 Dihedral : 6.489 44.417 3762 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.32 % Allowed : 4.15 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.13), residues: 3438 helix: -1.40 (0.12), residues: 1614 sheet: -1.34 (0.26), residues: 396 loop : -3.09 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 674 HIS 0.014 0.002 HIS F 451 PHE 0.020 0.002 PHE B 436 TYR 0.020 0.002 TYR F1158 ARG 0.017 0.001 ARG F 416 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 1115) hydrogen bonds : angle 5.18659 ( 3306) covalent geometry : bond 0.00411 (28404) covalent geometry : angle 0.75172 (38466) *********************** 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 588 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 578 time to evaluate : 3.052 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: A 281 MET cc_start: 0.9111 (tpp) cc_final: 0.8635 (tpp) REVERT: A 314 THR cc_start: 0.9204 (p) cc_final: 0.8574 (p) REVERT: A 318 ARG cc_start: 0.9355 (mtm-85) cc_final: 0.8843 (mmp80) REVERT: A 320 LEU cc_start: 0.9638 (mt) cc_final: 0.9149 (mt) REVERT: A 334 TYR cc_start: 0.8310 (m-80) cc_final: 0.8101 (m-80) REVERT: A 653 HIS cc_start: 0.9486 (m-70) cc_final: 0.9116 (m90) REVERT: A 658 VAL cc_start: 0.9358 (p) cc_final: 0.8971 (p) REVERT: A 701 PHE cc_start: 0.9313 (t80) cc_final: 0.8667 (t80) REVERT: A 704 LEU cc_start: 0.9514 (tp) cc_final: 0.9245 (mm) REVERT: A 741 PHE cc_start: 0.9121 (m-80) cc_final: 0.8895 (m-80) REVERT: A 1157 LEU cc_start: 0.9495 (mm) cc_final: 0.9274 (pp) REVERT: B 288 TYR cc_start: 0.9271 (m-80) cc_final: 0.8859 (m-80) REVERT: B 399 MET cc_start: 0.9235 (mmp) cc_final: 0.8945 (mmp) REVERT: B 405 ARG cc_start: 0.8223 (ptt180) cc_final: 0.7505 (mtm110) REVERT: B 411 ILE cc_start: 0.9520 (mp) cc_final: 0.9308 (mp) REVERT: B 469 GLU cc_start: 0.9633 (pt0) cc_final: 0.9432 (pt0) REVERT: B 519 PHE cc_start: 0.9527 (m-80) cc_final: 0.9151 (m-80) REVERT: B 521 MET cc_start: 0.9600 (mtm) cc_final: 0.9198 (mtp) REVERT: B 564 MET cc_start: 0.9300 (ttp) cc_final: 0.8986 (ppp) REVERT: B 630 HIS cc_start: 0.9584 (t70) cc_final: 0.9104 (t70) REVERT: B 653 HIS cc_start: 0.9578 (m90) cc_final: 0.9278 (m-70) REVERT: B 691 GLU cc_start: 0.9371 (tm-30) cc_final: 0.9110 (tm-30) REVERT: B 693 LEU cc_start: 0.9665 (mp) cc_final: 0.9289 (mp) REVERT: B 740 PHE cc_start: 0.9111 (t80) cc_final: 0.8849 (t80) REVERT: B 1185 MET cc_start: 0.9150 (mtt) cc_final: 0.8894 (mmt) REVERT: C 266 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8535 (tm-30) REVERT: C 320 LEU cc_start: 0.8738 (mt) cc_final: 0.8165 (mt) REVERT: C 356 LEU cc_start: 0.9593 (mt) cc_final: 0.9363 (mt) REVERT: C 399 MET cc_start: 0.9494 (mmp) cc_final: 0.8322 (tmm) REVERT: C 441 ARG cc_start: 0.9108 (tpp80) cc_final: 0.8882 (tpp80) REVERT: C 442 ASP cc_start: 0.9550 (p0) cc_final: 0.9138 (p0) REVERT: C 452 THR cc_start: 0.8928 (p) cc_final: 0.8504 (p) REVERT: C 480 ARG cc_start: 0.9612 (mmt90) cc_final: 0.9031 (mmm-85) REVERT: C 521 MET cc_start: 0.9567 (mtm) cc_final: 0.9237 (mtp) REVERT: C 654 LEU cc_start: 0.9429 (tp) cc_final: 0.9172 (tp) REVERT: C 1152 HIS cc_start: 0.9348 (m170) cc_final: 0.8747 (m-70) REVERT: D 283 MET cc_start: 0.8591 (ptt) cc_final: 0.8134 (ptt) REVERT: D 351 ARG cc_start: 0.9349 (mmm160) cc_final: 0.8857 (ttt180) REVERT: D 355 LEU cc_start: 0.9802 (mm) cc_final: 0.9550 (pp) REVERT: D 479 LEU cc_start: 0.9434 (mt) cc_final: 0.9022 (tp) REVERT: D 591 ARG cc_start: 0.9310 (mtt90) cc_final: 0.8992 (mtt-85) REVERT: D 636 MET cc_start: 0.9646 (pmm) cc_final: 0.9426 (pmm) REVERT: E 335 MET cc_start: 0.9493 (mmp) cc_final: 0.9142 (mmp) REVERT: E 591 ARG cc_start: 0.8737 (mtt90) cc_final: 0.8102 (mmp80) REVERT: E 592 LEU cc_start: 0.9380 (pt) cc_final: 0.9042 (pt) REVERT: E 636 MET cc_start: 0.9569 (mpp) cc_final: 0.9336 (mmt) REVERT: E 641 GLN cc_start: 0.9416 (pp30) cc_final: 0.9200 (pp30) REVERT: E 653 HIS cc_start: 0.9846 (m90) cc_final: 0.9486 (m-70) REVERT: E 697 ASP cc_start: 0.9249 (m-30) cc_final: 0.9004 (m-30) REVERT: E 701 PHE cc_start: 0.9525 (t80) cc_final: 0.8740 (t80) REVERT: F 297 MET cc_start: 0.9393 (ptt) cc_final: 0.8731 (mmm) REVERT: F 298 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8452 (pp30) REVERT: F 303 VAL cc_start: 0.9384 (t) cc_final: 0.9058 (t) REVERT: F 370 PHE cc_start: 0.9149 (m-80) cc_final: 0.8867 (m-80) REVERT: F 451 HIS cc_start: 0.9099 (m-70) cc_final: 0.8648 (m-70) REVERT: F 592 LEU cc_start: 0.9652 (pt) cc_final: 0.9417 (pt) REVERT: F 622 ILE cc_start: 0.9086 (pt) cc_final: 0.8854 (pt) REVERT: F 636 MET cc_start: 0.9304 (mpp) cc_final: 0.9077 (mmt) REVERT: F 656 LEU cc_start: 0.9644 (tt) cc_final: 0.9434 (tp) REVERT: F 660 ARG cc_start: 0.9623 (mmp-170) cc_final: 0.9374 (mmm-85) REVERT: F 673 ASN cc_start: 0.9402 (t0) cc_final: 0.9159 (m-40) REVERT: F 689 MET cc_start: 0.9750 (mmm) cc_final: 0.9357 (mmm) REVERT: F 727 TYR cc_start: 0.8425 (t80) cc_final: 0.8171 (t80) REVERT: F 741 PHE cc_start: 0.9240 (m-80) cc_final: 0.8792 (m-10) outliers start: 10 outliers final: 2 residues processed: 583 average time/residue: 0.4624 time to fit residues: 400.5266 Evaluate side-chains 415 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 413 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 122 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 285 optimal weight: 10.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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 A1154 HIS ** 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 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 661 HIS ** D 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 GLN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 ASN ** F 451 HIS ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.084201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059318 restraints weight = 184567.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.060616 restraints weight = 142033.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.061590 restraints weight = 116879.966| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28404 Z= 0.168 Angle : 0.725 10.358 38466 Z= 0.374 Chirality : 0.047 0.225 4302 Planarity : 0.006 0.083 4950 Dihedral : 6.231 41.566 3762 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.29 % Allowed : 4.02 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.13), residues: 3438 helix: -1.11 (0.12), residues: 1626 sheet: -1.33 (0.26), residues: 402 loop : -3.16 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 674 HIS 0.012 0.002 HIS F 451 PHE 0.035 0.002 PHE C 357 TYR 0.018 0.002 TYR F 601 ARG 0.017 0.001 ARG F 432 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 1115) hydrogen bonds : angle 4.97536 ( 3306) covalent geometry : bond 0.00355 (28404) covalent geometry : angle 0.72512 (38466) *********************** 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 563 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 554 time to evaluate : 3.097 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 281 MET cc_start: 0.8957 (tpp) cc_final: 0.8606 (tmm) REVERT: A 283 MET cc_start: 0.9289 (ppp) cc_final: 0.8999 (ppp) REVERT: A 314 THR cc_start: 0.9223 (p) cc_final: 0.8581 (p) REVERT: A 316 MET cc_start: 0.9646 (tpt) cc_final: 0.9288 (tpp) REVERT: A 318 ARG cc_start: 0.9313 (mtm-85) cc_final: 0.8841 (mmp80) REVERT: A 371 ASP cc_start: 0.9598 (t0) cc_final: 0.9289 (m-30) REVERT: A 410 ILE cc_start: 0.9193 (mt) cc_final: 0.8956 (mt) REVERT: A 596 GLU cc_start: 0.9490 (tp30) cc_final: 0.9187 (mm-30) REVERT: A 653 HIS cc_start: 0.9492 (m-70) cc_final: 0.9141 (m-70) REVERT: A 693 LEU cc_start: 0.8945 (mm) cc_final: 0.8664 (mm) REVERT: A 701 PHE cc_start: 0.9368 (t80) cc_final: 0.8921 (t80) REVERT: A 704 LEU cc_start: 0.9559 (tp) cc_final: 0.9235 (mm) REVERT: A 741 PHE cc_start: 0.9137 (m-80) cc_final: 0.8915 (m-80) REVERT: A 1157 LEU cc_start: 0.9479 (mm) cc_final: 0.9261 (pp) REVERT: B 288 TYR cc_start: 0.9337 (m-80) cc_final: 0.8970 (m-80) REVERT: B 305 PHE cc_start: 0.9481 (m-10) cc_final: 0.8981 (m-10) REVERT: B 405 ARG cc_start: 0.8292 (ptt180) cc_final: 0.7656 (mtm180) REVERT: B 469 GLU cc_start: 0.9636 (pt0) cc_final: 0.9387 (pt0) REVERT: B 519 PHE cc_start: 0.9513 (m-80) cc_final: 0.9152 (m-80) REVERT: B 521 MET cc_start: 0.9592 (mtm) cc_final: 0.9145 (mtp) REVERT: B 564 MET cc_start: 0.9278 (ttp) cc_final: 0.8877 (tmm) REVERT: B 595 PHE cc_start: 0.9275 (m-80) cc_final: 0.9073 (m-10) REVERT: B 630 HIS cc_start: 0.9609 (t70) cc_final: 0.9155 (t70) REVERT: B 653 HIS cc_start: 0.9636 (m90) cc_final: 0.9304 (m-70) REVERT: B 1185 MET cc_start: 0.9131 (mtt) cc_final: 0.8892 (mmt) REVERT: C 266 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8509 (tm-30) REVERT: C 320 LEU cc_start: 0.8748 (mt) cc_final: 0.8187 (mt) REVERT: C 334 TYR cc_start: 0.8510 (m-80) cc_final: 0.8030 (m-80) REVERT: C 356 LEU cc_start: 0.9545 (mt) cc_final: 0.9211 (mt) REVERT: C 399 MET cc_start: 0.9485 (mmp) cc_final: 0.8588 (ttm) REVERT: C 402 MET cc_start: 0.9363 (tmm) cc_final: 0.9147 (ppp) REVERT: C 441 ARG cc_start: 0.9025 (tpp80) cc_final: 0.8788 (tpp80) REVERT: C 442 ASP cc_start: 0.9538 (p0) cc_final: 0.9330 (p0) REVERT: C 480 ARG cc_start: 0.9650 (mmt90) cc_final: 0.9047 (mmm-85) REVERT: C 521 MET cc_start: 0.9532 (mtm) cc_final: 0.9180 (mtp) REVERT: C 689 MET cc_start: 0.9429 (mmp) cc_final: 0.9226 (mmm) REVERT: D 283 MET cc_start: 0.8706 (ptt) cc_final: 0.8269 (ptt) REVERT: D 351 ARG cc_start: 0.9365 (mmm160) cc_final: 0.8968 (ttt180) REVERT: D 430 PHE cc_start: 0.8545 (m-10) cc_final: 0.8212 (m-80) REVERT: D 591 ARG cc_start: 0.9335 (mtt90) cc_final: 0.9006 (mtt-85) REVERT: D 636 MET cc_start: 0.9657 (pmm) cc_final: 0.9453 (pmm) REVERT: D 656 LEU cc_start: 0.9870 (tp) cc_final: 0.9629 (tp) REVERT: E 328 ASN cc_start: 0.8724 (t0) cc_final: 0.8292 (p0) REVERT: E 399 MET cc_start: 0.8534 (mmp) cc_final: 0.8294 (mmp) REVERT: E 591 ARG cc_start: 0.8750 (mtt90) cc_final: 0.8424 (mtt-85) REVERT: E 592 LEU cc_start: 0.9371 (pt) cc_final: 0.9052 (pt) REVERT: E 641 GLN cc_start: 0.9428 (pp30) cc_final: 0.9224 (pp30) REVERT: E 653 HIS cc_start: 0.9818 (m90) cc_final: 0.9614 (m-70) REVERT: E 697 ASP cc_start: 0.9270 (m-30) cc_final: 0.9014 (m-30) REVERT: E 701 PHE cc_start: 0.9507 (t80) cc_final: 0.8762 (t80) REVERT: F 298 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8127 (pp30) REVERT: F 451 HIS cc_start: 0.9013 (m-70) cc_final: 0.8594 (m-70) REVERT: F 592 LEU cc_start: 0.9640 (pt) cc_final: 0.9429 (pt) REVERT: F 622 ILE cc_start: 0.9156 (pt) cc_final: 0.8923 (pt) REVERT: F 657 GLU cc_start: 0.9537 (mp0) cc_final: 0.9228 (mp0) REVERT: F 673 ASN cc_start: 0.9457 (t0) cc_final: 0.9199 (m-40) REVERT: F 689 MET cc_start: 0.9760 (mmm) cc_final: 0.9388 (mmm) REVERT: F 741 PHE cc_start: 0.9189 (m-80) cc_final: 0.8696 (m-10) outliers start: 9 outliers final: 1 residues processed: 562 average time/residue: 0.4298 time to fit residues: 364.6807 Evaluate side-chains 395 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 394 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 340 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 328 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 260 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 329 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 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 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 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1152 HIS ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN D 661 HIS ** D 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 GLN ** E 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 661 HIS ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 661 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.082763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.058123 restraints weight = 178041.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.059378 restraints weight = 137011.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.060328 restraints weight = 112926.247| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28404 Z= 0.171 Angle : 0.722 8.917 38466 Z= 0.373 Chirality : 0.047 0.230 4302 Planarity : 0.006 0.076 4950 Dihedral : 6.108 41.514 3762 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.13), residues: 3438 helix: -0.98 (0.12), residues: 1614 sheet: -1.40 (0.26), residues: 402 loop : -3.05 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 674 HIS 0.010 0.002 HIS F 451 PHE 0.019 0.002 PHE D 720 TYR 0.023 0.002 TYR F1158 ARG 0.009 0.001 ARG E 429 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 1115) hydrogen bonds : angle 5.04218 ( 3306) covalent geometry : bond 0.00365 (28404) covalent geometry : angle 0.72163 (38466) *********************** 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 531 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 530 time to evaluate : 3.071 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 281 MET cc_start: 0.9050 (tpp) cc_final: 0.8439 (tpp) REVERT: A 316 MET cc_start: 0.9678 (tpt) cc_final: 0.9410 (tpp) REVERT: A 334 TYR cc_start: 0.8445 (m-80) cc_final: 0.8182 (m-80) REVERT: A 371 ASP cc_start: 0.9606 (t0) cc_final: 0.9311 (m-30) REVERT: A 410 ILE cc_start: 0.9231 (mt) cc_final: 0.9016 (mt) REVERT: A 596 GLU cc_start: 0.9398 (tp30) cc_final: 0.9103 (mm-30) REVERT: A 640 LEU cc_start: 0.9613 (mm) cc_final: 0.8929 (tp) REVERT: A 653 HIS cc_start: 0.9536 (m-70) cc_final: 0.9251 (m-70) REVERT: A 657 GLU cc_start: 0.9558 (mp0) cc_final: 0.9307 (mp0) REVERT: A 741 PHE cc_start: 0.9212 (m-80) cc_final: 0.8987 (m-80) REVERT: A 1152 HIS cc_start: 0.9784 (m90) cc_final: 0.9299 (m-70) REVERT: A 1157 LEU cc_start: 0.9490 (mm) cc_final: 0.9252 (pp) REVERT: B 320 LEU cc_start: 0.9306 (mt) cc_final: 0.9098 (mt) REVERT: B 405 ARG cc_start: 0.8214 (ptt180) cc_final: 0.7872 (mtm110) REVERT: B 411 ILE cc_start: 0.9636 (mp) cc_final: 0.9380 (mp) REVERT: B 469 GLU cc_start: 0.9662 (pt0) cc_final: 0.9423 (pt0) REVERT: B 519 PHE cc_start: 0.9511 (m-80) cc_final: 0.9167 (m-80) REVERT: B 521 MET cc_start: 0.9593 (mtm) cc_final: 0.9148 (mtp) REVERT: B 564 MET cc_start: 0.9293 (ttp) cc_final: 0.8941 (ppp) REVERT: B 595 PHE cc_start: 0.9354 (m-80) cc_final: 0.9135 (m-10) REVERT: B 630 HIS cc_start: 0.9595 (t70) cc_final: 0.9139 (t70) REVERT: B 653 HIS cc_start: 0.9607 (m90) cc_final: 0.9331 (m-70) REVERT: B 658 VAL cc_start: 0.9254 (m) cc_final: 0.9030 (m) REVERT: B 740 PHE cc_start: 0.9166 (t80) cc_final: 0.8925 (t80) REVERT: C 266 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8414 (tm-30) REVERT: C 320 LEU cc_start: 0.8752 (mt) cc_final: 0.8207 (mt) REVERT: C 334 TYR cc_start: 0.8530 (m-80) cc_final: 0.8049 (m-80) REVERT: C 402 MET cc_start: 0.9387 (tmm) cc_final: 0.9154 (ppp) REVERT: C 441 ARG cc_start: 0.9007 (tpp80) cc_final: 0.8771 (tpp80) REVERT: C 442 ASP cc_start: 0.9571 (p0) cc_final: 0.9346 (p0) REVERT: C 521 MET cc_start: 0.9533 (mtm) cc_final: 0.9165 (mtp) REVERT: C 592 LEU cc_start: 0.9454 (pt) cc_final: 0.9235 (pt) REVERT: D 283 MET cc_start: 0.8740 (ptt) cc_final: 0.8388 (ptt) REVERT: D 351 ARG cc_start: 0.9394 (mmm160) cc_final: 0.8995 (ttt180) REVERT: D 370 PHE cc_start: 0.8596 (m-80) cc_final: 0.8328 (m-80) REVERT: D 371 ASP cc_start: 0.9598 (m-30) cc_final: 0.9287 (p0) REVERT: D 591 ARG cc_start: 0.9337 (mtt90) cc_final: 0.9054 (mtt-85) REVERT: D 656 LEU cc_start: 0.9855 (tp) cc_final: 0.9491 (tp) REVERT: E 328 ASN cc_start: 0.8799 (t0) cc_final: 0.8454 (p0) REVERT: E 592 LEU cc_start: 0.9404 (pt) cc_final: 0.9114 (pt) REVERT: E 636 MET cc_start: 0.9515 (mpp) cc_final: 0.8737 (mmm) REVERT: E 639 LEU cc_start: 0.9833 (mt) cc_final: 0.9618 (mt) REVERT: E 653 HIS cc_start: 0.9819 (m90) cc_final: 0.9534 (m-70) REVERT: E 674 TRP cc_start: 0.8980 (t60) cc_final: 0.8572 (t-100) REVERT: E 697 ASP cc_start: 0.9203 (m-30) cc_final: 0.8954 (m-30) REVERT: E 701 PHE cc_start: 0.9630 (t80) cc_final: 0.8878 (t80) REVERT: F 298 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7711 (tp40) REVERT: F 328 ASN cc_start: 0.7868 (m-40) cc_final: 0.7430 (p0) REVERT: F 370 PHE cc_start: 0.9080 (m-80) cc_final: 0.8804 (m-80) REVERT: F 451 HIS cc_start: 0.8961 (m-70) cc_final: 0.8523 (m-70) REVERT: F 592 LEU cc_start: 0.9650 (pt) cc_final: 0.9415 (pt) REVERT: F 601 TYR cc_start: 0.8271 (t80) cc_final: 0.8013 (t80) REVERT: F 657 GLU cc_start: 0.9490 (mp0) cc_final: 0.9258 (mp0) REVERT: F 673 ASN cc_start: 0.9488 (t0) cc_final: 0.9237 (m-40) REVERT: F 689 MET cc_start: 0.9775 (mmm) cc_final: 0.9396 (mmm) REVERT: F 741 PHE cc_start: 0.9203 (m-80) cc_final: 0.8699 (m-10) outliers start: 1 outliers final: 0 residues processed: 531 average time/residue: 0.4226 time to fit residues: 344.8325 Evaluate side-chains 404 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 182 optimal weight: 8.9990 chunk 314 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 253 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 318 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN C 352 GLN C 364 GLN C 489 ASN C 506 GLN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1152 HIS ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN D 724 GLN E 277 GLN E 364 GLN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 661 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.058689 restraints weight = 184339.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060027 restraints weight = 140030.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.060994 restraints weight = 114477.024| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28404 Z= 0.140 Angle : 0.704 9.989 38466 Z= 0.359 Chirality : 0.047 0.361 4302 Planarity : 0.006 0.071 4950 Dihedral : 5.935 41.352 3762 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.14), residues: 3438 helix: -0.77 (0.12), residues: 1608 sheet: -1.15 (0.26), residues: 390 loop : -2.90 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 674 HIS 0.009 0.001 HIS E1154 PHE 0.020 0.001 PHE B 553 TYR 0.024 0.002 TYR E1158 ARG 0.007 0.001 ARG E1179 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 1115) hydrogen bonds : angle 4.82629 ( 3306) covalent geometry : bond 0.00298 (28404) covalent geometry : angle 0.70440 (38466) *********************** 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 544 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 543 time to evaluate : 3.529 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 281 MET cc_start: 0.9134 (tpp) cc_final: 0.8905 (tpp) REVERT: A 316 MET cc_start: 0.9687 (tpt) cc_final: 0.9375 (tpp) REVERT: A 320 LEU cc_start: 0.9694 (mt) cc_final: 0.9453 (mt) REVERT: A 334 TYR cc_start: 0.8396 (m-80) cc_final: 0.8079 (m-80) REVERT: A 596 GLU cc_start: 0.9354 (tp30) cc_final: 0.9118 (mm-30) REVERT: A 653 HIS cc_start: 0.9564 (m-70) cc_final: 0.9253 (m-70) REVERT: A 741 PHE cc_start: 0.9170 (m-80) cc_final: 0.8938 (m-80) REVERT: A 1152 HIS cc_start: 0.9781 (m90) cc_final: 0.9264 (m-70) REVERT: A 1157 LEU cc_start: 0.9479 (mm) cc_final: 0.9244 (pp) REVERT: B 320 LEU cc_start: 0.9328 (mt) cc_final: 0.9101 (mt) REVERT: B 405 ARG cc_start: 0.8140 (ptt180) cc_final: 0.7874 (mtm110) REVERT: B 411 ILE cc_start: 0.9652 (mp) cc_final: 0.9425 (mp) REVERT: B 469 GLU cc_start: 0.9692 (pt0) cc_final: 0.9482 (pt0) REVERT: B 519 PHE cc_start: 0.9544 (m-80) cc_final: 0.9224 (m-80) REVERT: B 521 MET cc_start: 0.9596 (mtm) cc_final: 0.9126 (mtp) REVERT: B 564 MET cc_start: 0.9255 (ttp) cc_final: 0.8939 (ppp) REVERT: B 595 PHE cc_start: 0.9337 (m-80) cc_final: 0.9072 (m-10) REVERT: B 630 HIS cc_start: 0.9582 (t70) cc_final: 0.9014 (t-90) REVERT: B 636 MET cc_start: 0.9530 (mpp) cc_final: 0.9289 (mpp) REVERT: B 653 HIS cc_start: 0.9603 (m90) cc_final: 0.9311 (m-70) REVERT: B 658 VAL cc_start: 0.9298 (m) cc_final: 0.9052 (m) REVERT: C 266 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8475 (tm-30) REVERT: C 320 LEU cc_start: 0.8751 (mt) cc_final: 0.8207 (mt) REVERT: C 334 TYR cc_start: 0.8482 (m-80) cc_final: 0.7999 (m-80) REVERT: C 402 MET cc_start: 0.9362 (tmm) cc_final: 0.9127 (ppp) REVERT: C 442 ASP cc_start: 0.9552 (p0) cc_final: 0.9340 (p0) REVERT: C 480 ARG cc_start: 0.9654 (mmt90) cc_final: 0.9066 (mmm-85) REVERT: C 592 LEU cc_start: 0.9419 (pt) cc_final: 0.9071 (pt) REVERT: C 631 VAL cc_start: 0.8728 (m) cc_final: 0.8408 (t) REVERT: C 636 MET cc_start: 0.9131 (pmm) cc_final: 0.8701 (pmm) REVERT: C 689 MET cc_start: 0.9423 (mmp) cc_final: 0.9194 (mmm) REVERT: D 283 MET cc_start: 0.8848 (ptt) cc_final: 0.8484 (ptt) REVERT: D 351 ARG cc_start: 0.9393 (mmm160) cc_final: 0.9037 (ttt180) REVERT: D 370 PHE cc_start: 0.8899 (m-80) cc_final: 0.8668 (m-80) REVERT: D 371 ASP cc_start: 0.9610 (m-30) cc_final: 0.9335 (p0) REVERT: D 470 LYS cc_start: 0.9343 (mtmt) cc_final: 0.9141 (mtpt) REVERT: D 591 ARG cc_start: 0.9343 (mtt90) cc_final: 0.9077 (mtt-85) REVERT: D 592 LEU cc_start: 0.8997 (mm) cc_final: 0.8609 (mm) REVERT: D 641 GLN cc_start: 0.9553 (pt0) cc_final: 0.9334 (pt0) REVERT: D 656 LEU cc_start: 0.9850 (tp) cc_final: 0.9553 (tp) REVERT: E 328 ASN cc_start: 0.8820 (t0) cc_final: 0.8343 (p0) REVERT: E 592 LEU cc_start: 0.9412 (pt) cc_final: 0.9123 (pt) REVERT: E 636 MET cc_start: 0.9592 (mpp) cc_final: 0.8891 (mpp) REVERT: E 639 LEU cc_start: 0.9838 (mt) cc_final: 0.9626 (mt) REVERT: E 641 GLN cc_start: 0.9383 (pp30) cc_final: 0.9134 (pt0) REVERT: E 674 TRP cc_start: 0.8912 (t60) cc_final: 0.8702 (t-100) REVERT: E 701 PHE cc_start: 0.9599 (t80) cc_final: 0.8907 (t80) REVERT: E 741 PHE cc_start: 0.9495 (m-80) cc_final: 0.9251 (m-80) REVERT: F 298 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7855 (tp40) REVERT: F 370 PHE cc_start: 0.9122 (m-80) cc_final: 0.8813 (m-80) REVERT: F 402 MET cc_start: 0.7608 (mtt) cc_final: 0.7318 (mtt) REVERT: F 451 HIS cc_start: 0.8965 (m-70) cc_final: 0.8593 (m-70) REVERT: F 592 LEU cc_start: 0.9637 (pt) cc_final: 0.9349 (pt) REVERT: F 601 TYR cc_start: 0.8362 (t80) cc_final: 0.7981 (t80) REVERT: F 657 GLU cc_start: 0.9497 (mp0) cc_final: 0.9178 (mp0) REVERT: F 689 MET cc_start: 0.9784 (mmm) cc_final: 0.9428 (mmm) REVERT: F 741 PHE cc_start: 0.9187 (m-80) cc_final: 0.8659 (m-10) outliers start: 1 outliers final: 0 residues processed: 544 average time/residue: 0.4386 time to fit residues: 366.6956 Evaluate side-chains 418 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 138 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 284 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.0670 chunk 190 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 313 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- 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 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 506 GLN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1152 HIS ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN E 277 GLN ** 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 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 615 GLN F 661 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.083724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.058997 restraints weight = 174877.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.060286 restraints weight = 134807.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061252 restraints weight = 110787.648| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28404 Z= 0.128 Angle : 0.716 9.940 38466 Z= 0.363 Chirality : 0.047 0.294 4302 Planarity : 0.006 0.071 4950 Dihedral : 5.739 40.653 3762 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.14), residues: 3438 helix: -0.71 (0.13), residues: 1626 sheet: -1.19 (0.26), residues: 402 loop : -2.90 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 674 HIS 0.015 0.001 HIS C 661 PHE 0.021 0.001 PHE B 553 TYR 0.030 0.001 TYR B1158 ARG 0.007 0.001 ARG E1179 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 1115) hydrogen bonds : angle 4.86058 ( 3306) covalent geometry : bond 0.00276 (28404) covalent geometry : angle 0.71600 (38466) *********************** 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 : 3.299 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 281 MET cc_start: 0.9175 (tpp) cc_final: 0.8674 (tpp) REVERT: A 371 ASP cc_start: 0.9619 (t0) cc_final: 0.9265 (m-30) REVERT: A 596 GLU cc_start: 0.9328 (tp30) cc_final: 0.9083 (mm-30) REVERT: A 653 HIS cc_start: 0.9545 (m-70) cc_final: 0.9277 (m-70) REVERT: A 673 ASN cc_start: 0.9552 (t0) cc_final: 0.9339 (t0) REVERT: A 689 MET cc_start: 0.9678 (tpp) cc_final: 0.9359 (tpp) REVERT: A 729 LEU cc_start: 0.9433 (mt) cc_final: 0.9225 (mt) REVERT: A 741 PHE cc_start: 0.9192 (m-80) cc_final: 0.8974 (m-80) REVERT: A 1152 HIS cc_start: 0.9783 (m90) cc_final: 0.9283 (m-70) REVERT: A 1157 LEU cc_start: 0.9480 (mm) cc_final: 0.9240 (pp) REVERT: B 288 TYR cc_start: 0.9415 (m-10) cc_final: 0.9070 (m-80) REVERT: B 318 ARG cc_start: 0.9373 (tpm170) cc_final: 0.9098 (tpm170) REVERT: B 320 LEU cc_start: 0.9379 (mt) cc_final: 0.9138 (mt) REVERT: B 411 ILE cc_start: 0.9624 (mp) cc_final: 0.9370 (mp) REVERT: B 469 GLU cc_start: 0.9702 (pt0) cc_final: 0.9489 (pt0) REVERT: B 519 PHE cc_start: 0.9539 (m-80) cc_final: 0.9236 (m-80) REVERT: B 521 MET cc_start: 0.9609 (mtm) cc_final: 0.9143 (mtp) REVERT: B 532 ARG cc_start: 0.8622 (mmp-170) cc_final: 0.8410 (mmm160) REVERT: B 564 MET cc_start: 0.9219 (ttp) cc_final: 0.8988 (tmm) REVERT: B 595 PHE cc_start: 0.9349 (m-80) cc_final: 0.9090 (m-10) REVERT: B 630 HIS cc_start: 0.9582 (t70) cc_final: 0.9061 (t-90) REVERT: B 653 HIS cc_start: 0.9591 (m90) cc_final: 0.9260 (m-70) REVERT: B 658 VAL cc_start: 0.9226 (m) cc_final: 0.8975 (m) REVERT: B 740 PHE cc_start: 0.9107 (t80) cc_final: 0.8823 (t80) REVERT: B 1185 MET cc_start: 0.9144 (mtt) cc_final: 0.8663 (mmm) REVERT: C 266 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8474 (tm-30) REVERT: C 320 LEU cc_start: 0.8744 (mt) cc_final: 0.8208 (mt) REVERT: C 442 ASP cc_start: 0.9511 (p0) cc_final: 0.9286 (p0) REVERT: C 480 ARG cc_start: 0.9659 (mmt90) cc_final: 0.9133 (mmm-85) REVERT: C 519 PHE cc_start: 0.9429 (m-80) cc_final: 0.9091 (m-80) REVERT: C 592 LEU cc_start: 0.9447 (pt) cc_final: 0.8986 (pt) REVERT: C 636 MET cc_start: 0.9117 (pmm) cc_final: 0.8727 (pmm) REVERT: C 689 MET cc_start: 0.9405 (mmp) cc_final: 0.9135 (mmm) REVERT: D 283 MET cc_start: 0.8803 (ptt) cc_final: 0.8428 (ptt) REVERT: D 351 ARG cc_start: 0.9368 (mmm160) cc_final: 0.9025 (ttt180) REVERT: D 370 PHE cc_start: 0.8969 (m-80) cc_final: 0.8712 (m-80) REVERT: D 371 ASP cc_start: 0.9582 (m-30) cc_final: 0.9288 (p0) REVERT: D 592 LEU cc_start: 0.9020 (mm) cc_final: 0.8680 (mm) REVERT: D 656 LEU cc_start: 0.9835 (tp) cc_final: 0.9561 (tp) REVERT: D 660 ARG cc_start: 0.8981 (ptt-90) cc_final: 0.8590 (ptt90) REVERT: E 328 ASN cc_start: 0.8757 (t0) cc_final: 0.8371 (p0) REVERT: E 636 MET cc_start: 0.9566 (mpp) cc_final: 0.9276 (mmm) REVERT: E 653 HIS cc_start: 0.9876 (m90) cc_final: 0.9666 (m-70) REVERT: E 674 TRP cc_start: 0.8907 (t60) cc_final: 0.8574 (t60) REVERT: E 686 PHE cc_start: 0.9581 (t80) cc_final: 0.9347 (t80) REVERT: E 697 ASP cc_start: 0.9183 (m-30) cc_final: 0.8962 (m-30) REVERT: E 701 PHE cc_start: 0.9621 (t80) cc_final: 0.8955 (t80) REVERT: E 741 PHE cc_start: 0.9455 (m-80) cc_final: 0.9244 (m-80) REVERT: F 298 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7746 (tp40) REVERT: F 370 PHE cc_start: 0.9079 (m-80) cc_final: 0.8737 (m-80) REVERT: F 402 MET cc_start: 0.7547 (mtt) cc_final: 0.7327 (mtt) REVERT: F 451 HIS cc_start: 0.8973 (m-70) cc_final: 0.8518 (m-70) REVERT: F 601 TYR cc_start: 0.8365 (t80) cc_final: 0.8104 (t80) REVERT: F 640 LEU cc_start: 0.9032 (mm) cc_final: 0.8790 (mm) REVERT: F 645 GLN cc_start: 0.9241 (pt0) cc_final: 0.8620 (pt0) REVERT: F 653 HIS cc_start: 0.9599 (m170) cc_final: 0.9094 (m170) REVERT: F 674 TRP cc_start: 0.9530 (t-100) cc_final: 0.9136 (t-100) REVERT: F 689 MET cc_start: 0.9777 (mmm) cc_final: 0.9311 (mmm) REVERT: F 741 PHE cc_start: 0.9115 (m-80) cc_final: 0.8590 (m-10) REVERT: F 1156 PHE cc_start: 0.9677 (m-10) cc_final: 0.9448 (m-10) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.4347 time to fit residues: 360.6147 Evaluate side-chains 424 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 286 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 150 optimal weight: 0.4980 chunk 270 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 615 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 388 HIS C 489 ASN C 506 GLN C1152 HIS D 489 ASN ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 GLN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 661 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.079545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.055269 restraints weight = 187792.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.056537 restraints weight = 142617.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.057342 restraints weight = 116966.064| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28404 Z= 0.145 Angle : 0.726 8.615 38466 Z= 0.371 Chirality : 0.047 0.299 4302 Planarity : 0.006 0.069 4950 Dihedral : 5.700 40.224 3762 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.14), residues: 3438 helix: -0.72 (0.13), residues: 1632 sheet: -1.21 (0.26), residues: 402 loop : -2.81 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 674 HIS 0.008 0.001 HIS F 451 PHE 0.022 0.002 PHE B 553 TYR 0.029 0.002 TYR F1158 ARG 0.010 0.001 ARG E1179 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 1115) hydrogen bonds : angle 4.96222 ( 3306) covalent geometry : bond 0.00313 (28404) covalent geometry : angle 0.72558 (38466) *********************** 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 521 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 3.218 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 281 MET cc_start: 0.9160 (tpp) cc_final: 0.8930 (tpp) REVERT: A 316 MET cc_start: 0.9752 (mmp) cc_final: 0.9532 (mmm) REVERT: A 334 TYR cc_start: 0.8270 (m-80) cc_final: 0.8000 (m-80) REVERT: A 371 ASP cc_start: 0.9648 (t0) cc_final: 0.9304 (m-30) REVERT: A 596 GLU cc_start: 0.9333 (tp30) cc_final: 0.9101 (mm-30) REVERT: A 649 THR cc_start: 0.9673 (m) cc_final: 0.9209 (p) REVERT: A 653 HIS cc_start: 0.9539 (m-70) cc_final: 0.9323 (m90) REVERT: A 673 ASN cc_start: 0.9547 (t0) cc_final: 0.9307 (t0) REVERT: A 689 MET cc_start: 0.9685 (tpp) cc_final: 0.9106 (tpp) REVERT: A 704 LEU cc_start: 0.9623 (tp) cc_final: 0.9172 (mm) REVERT: A 741 PHE cc_start: 0.9172 (m-80) cc_final: 0.8970 (m-80) REVERT: A 1152 HIS cc_start: 0.9763 (m90) cc_final: 0.9237 (m-70) REVERT: A 1157 LEU cc_start: 0.9468 (mm) cc_final: 0.9218 (pp) REVERT: B 288 TYR cc_start: 0.9412 (m-10) cc_final: 0.9116 (m-80) REVERT: B 320 LEU cc_start: 0.9358 (mt) cc_final: 0.9091 (mt) REVERT: B 411 ILE cc_start: 0.9657 (mp) cc_final: 0.9438 (mp) REVERT: B 469 GLU cc_start: 0.9702 (pt0) cc_final: 0.9477 (pt0) REVERT: B 519 PHE cc_start: 0.9505 (m-80) cc_final: 0.9199 (m-80) REVERT: B 521 MET cc_start: 0.9623 (mtm) cc_final: 0.9152 (mtp) REVERT: B 564 MET cc_start: 0.9198 (ttp) cc_final: 0.8937 (tmm) REVERT: B 595 PHE cc_start: 0.9274 (m-80) cc_final: 0.9013 (m-10) REVERT: B 636 MET cc_start: 0.9541 (mmt) cc_final: 0.9336 (mmt) REVERT: B 658 VAL cc_start: 0.9172 (m) cc_final: 0.8920 (m) REVERT: B 1185 MET cc_start: 0.9080 (mtt) cc_final: 0.8653 (mmm) REVERT: C 266 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8485 (tm-30) REVERT: C 320 LEU cc_start: 0.8753 (mt) cc_final: 0.8216 (mt) REVERT: C 442 ASP cc_start: 0.9458 (p0) cc_final: 0.9243 (p0) REVERT: C 480 ARG cc_start: 0.9661 (mmt90) cc_final: 0.9135 (mmm-85) REVERT: C 519 PHE cc_start: 0.9363 (m-80) cc_final: 0.9073 (m-80) REVERT: C 523 MET cc_start: 0.9460 (tpp) cc_final: 0.9162 (tpp) REVERT: C 592 LEU cc_start: 0.9374 (pt) cc_final: 0.8951 (pt) REVERT: C 636 MET cc_start: 0.9128 (pmm) cc_final: 0.8699 (pmm) REVERT: C 689 MET cc_start: 0.9440 (mmp) cc_final: 0.9193 (mmm) REVERT: D 283 MET cc_start: 0.8874 (ptt) cc_final: 0.8540 (ptt) REVERT: D 351 ARG cc_start: 0.9419 (mmm160) cc_final: 0.9208 (ttt180) REVERT: D 370 PHE cc_start: 0.9026 (m-80) cc_final: 0.8816 (m-80) REVERT: D 371 ASP cc_start: 0.9654 (m-30) cc_final: 0.9441 (p0) REVERT: D 591 ARG cc_start: 0.9279 (mtt90) cc_final: 0.9037 (mtt-85) REVERT: D 592 LEU cc_start: 0.9039 (mm) cc_final: 0.8660 (mm) REVERT: D 641 GLN cc_start: 0.9514 (pt0) cc_final: 0.9232 (pt0) REVERT: E 316 MET cc_start: 0.9191 (mtm) cc_final: 0.8158 (tpp) REVERT: E 320 LEU cc_start: 0.9584 (mt) cc_final: 0.9135 (mt) REVERT: E 328 ASN cc_start: 0.8577 (t0) cc_final: 0.8198 (p0) REVERT: E 636 MET cc_start: 0.9582 (mpp) cc_final: 0.9234 (mmm) REVERT: E 674 TRP cc_start: 0.9049 (t60) cc_final: 0.8687 (t60) REVERT: E 697 ASP cc_start: 0.9173 (m-30) cc_final: 0.8940 (m-30) REVERT: E 701 PHE cc_start: 0.9637 (t80) cc_final: 0.8948 (t80) REVERT: E 741 PHE cc_start: 0.9362 (m-80) cc_final: 0.9157 (m-80) REVERT: F 370 PHE cc_start: 0.9165 (m-80) cc_final: 0.8864 (m-80) REVERT: F 451 HIS cc_start: 0.8944 (m-70) cc_final: 0.8527 (m-70) REVERT: F 645 GLN cc_start: 0.9204 (pt0) cc_final: 0.8901 (pt0) REVERT: F 689 MET cc_start: 0.9783 (mmm) cc_final: 0.9339 (mmm) REVERT: F 741 PHE cc_start: 0.9029 (m-80) cc_final: 0.8473 (m-10) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.4450 time to fit residues: 356.1102 Evaluate side-chains 409 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 3.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 71 optimal weight: 30.0000 chunk 254 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 175 optimal weight: 30.0000 chunk 315 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 227 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 489 ASN C 506 GLN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1152 HIS D 364 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN E 277 GLN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN ** F 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 HIS F 661 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.083514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.058958 restraints weight = 174949.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.060282 restraints weight = 133440.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.061284 restraints weight = 108599.084| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.6518 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= 0.127 Angle : 0.723 9.935 38466 Z= 0.367 Chirality : 0.048 0.232 4302 Planarity : 0.006 0.069 4950 Dihedral : 5.602 40.346 3762 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.14), residues: 3438 helix: -0.58 (0.13), residues: 1620 sheet: -1.19 (0.26), residues: 402 loop : -2.75 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 674 HIS 0.009 0.001 HIS B1154 PHE 0.024 0.001 PHE C 357 TYR 0.036 0.002 TYR B1158 ARG 0.012 0.001 ARG D 354 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 1115) hydrogen bonds : angle 4.91017 ( 3306) covalent geometry : bond 0.00274 (28404) covalent geometry : angle 0.72287 (38466) *********************** 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 529 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 2.940 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 274 TYR cc_start: 0.8568 (m-10) cc_final: 0.8354 (m-10) REVERT: A 281 MET cc_start: 0.9133 (tpp) cc_final: 0.8656 (tpp) REVERT: A 371 ASP cc_start: 0.9644 (t0) cc_final: 0.9284 (m-30) REVERT: A 410 ILE cc_start: 0.9091 (pt) cc_final: 0.8887 (pt) REVERT: A 596 GLU cc_start: 0.9351 (tp30) cc_final: 0.9125 (mm-30) REVERT: A 649 THR cc_start: 0.9671 (m) cc_final: 0.9228 (p) REVERT: A 653 HIS cc_start: 0.9507 (m-70) cc_final: 0.9247 (m-70) REVERT: A 673 ASN cc_start: 0.9572 (t0) cc_final: 0.9298 (t0) REVERT: A 689 MET cc_start: 0.9695 (tpp) cc_final: 0.9332 (tpp) REVERT: A 704 LEU cc_start: 0.9635 (tp) cc_final: 0.9253 (mm) REVERT: A 1152 HIS cc_start: 0.9788 (m90) cc_final: 0.9285 (m-70) REVERT: A 1157 LEU cc_start: 0.9488 (mm) cc_final: 0.9245 (pp) REVERT: B 288 TYR cc_start: 0.9380 (m-10) cc_final: 0.9104 (m-80) REVERT: B 318 ARG cc_start: 0.9422 (tpm170) cc_final: 0.9126 (tpm170) REVERT: B 320 LEU cc_start: 0.9410 (mt) cc_final: 0.9161 (mt) REVERT: B 411 ILE cc_start: 0.9633 (mp) cc_final: 0.9404 (mp) REVERT: B 469 GLU cc_start: 0.9662 (pt0) cc_final: 0.9421 (pt0) REVERT: B 521 MET cc_start: 0.9597 (mtm) cc_final: 0.9120 (mtp) REVERT: B 564 MET cc_start: 0.9190 (ttp) cc_final: 0.8977 (tmm) REVERT: B 595 PHE cc_start: 0.9317 (m-80) cc_final: 0.9038 (m-10) REVERT: B 636 MET cc_start: 0.9664 (mmt) cc_final: 0.9248 (mmp) REVERT: B 658 VAL cc_start: 0.9190 (m) cc_final: 0.8959 (m) REVERT: B 659 ARG cc_start: 0.8666 (ttt180) cc_final: 0.8406 (mtt180) REVERT: B 674 TRP cc_start: 0.8815 (t60) cc_final: 0.8390 (t60) REVERT: B 1185 MET cc_start: 0.8898 (mtt) cc_final: 0.8600 (mmm) REVERT: C 266 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8509 (tm-30) REVERT: C 320 LEU cc_start: 0.8732 (mt) cc_final: 0.8201 (mt) REVERT: C 399 MET cc_start: 0.9503 (mpp) cc_final: 0.8928 (ttt) REVERT: C 480 ARG cc_start: 0.9674 (mmt90) cc_final: 0.9152 (mmm-85) REVERT: C 519 PHE cc_start: 0.9417 (m-80) cc_final: 0.9120 (m-80) REVERT: C 523 MET cc_start: 0.9494 (tpp) cc_final: 0.9232 (tpp) REVERT: C 592 LEU cc_start: 0.9574 (pt) cc_final: 0.9345 (pt) REVERT: C 636 MET cc_start: 0.9084 (pmm) cc_final: 0.8783 (pmm) REVERT: C 689 MET cc_start: 0.9481 (mmp) cc_final: 0.9232 (mmm) REVERT: C 1152 HIS cc_start: 0.9128 (m170) cc_final: 0.8591 (m-70) REVERT: D 283 MET cc_start: 0.8869 (ptt) cc_final: 0.8476 (ptt) REVERT: D 351 ARG cc_start: 0.9387 (mmm160) cc_final: 0.9089 (ttt180) REVERT: D 370 PHE cc_start: 0.9014 (m-80) cc_final: 0.8722 (m-80) REVERT: D 371 ASP cc_start: 0.9552 (m-30) cc_final: 0.9239 (p0) REVERT: D 592 LEU cc_start: 0.9069 (mm) cc_final: 0.8757 (mm) REVERT: D 660 ARG cc_start: 0.9071 (ptt-90) cc_final: 0.8766 (ptt90) REVERT: E 316 MET cc_start: 0.9232 (mtm) cc_final: 0.8232 (tpp) REVERT: E 320 LEU cc_start: 0.9636 (mt) cc_final: 0.9280 (mt) REVERT: E 328 ASN cc_start: 0.8583 (t0) cc_final: 0.8255 (p0) REVERT: E 415 ASN cc_start: 0.8842 (p0) cc_final: 0.8324 (t0) REVERT: E 636 MET cc_start: 0.9604 (mpp) cc_final: 0.9326 (mmt) REVERT: E 674 TRP cc_start: 0.9017 (t60) cc_final: 0.8676 (t60) REVERT: E 697 ASP cc_start: 0.9085 (m-30) cc_final: 0.8817 (m-30) REVERT: E 701 PHE cc_start: 0.9653 (t80) cc_final: 0.8944 (t80) REVERT: F 370 PHE cc_start: 0.9074 (m-80) cc_final: 0.8717 (m-80) REVERT: F 451 HIS cc_start: 0.8920 (m-70) cc_final: 0.8502 (m-70) REVERT: F 601 TYR cc_start: 0.8429 (t80) cc_final: 0.8192 (t80) REVERT: F 606 LEU cc_start: 0.9520 (mt) cc_final: 0.9319 (mt) REVERT: F 645 GLN cc_start: 0.9459 (pt0) cc_final: 0.8876 (pt0) REVERT: F 653 HIS cc_start: 0.9472 (m90) cc_final: 0.9134 (m170) REVERT: F 657 GLU cc_start: 0.9556 (mp0) cc_final: 0.9293 (mp0) REVERT: F 689 MET cc_start: 0.9772 (mmm) cc_final: 0.9380 (mmm) REVERT: F 741 PHE cc_start: 0.9079 (m-80) cc_final: 0.8501 (m-10) REVERT: F 1156 PHE cc_start: 0.9695 (m-10) cc_final: 0.9472 (m-10) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.4364 time to fit residues: 355.2313 Evaluate side-chains 415 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 217 optimal weight: 0.8980 chunk 260 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 304 optimal weight: 6.9990 chunk 156 optimal weight: 0.0980 chunk 62 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 624 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 506 GLN C 388 HIS C 489 ASN C 506 GLN ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 GLN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 661 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.080231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.055763 restraints weight = 186640.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.057044 restraints weight = 141246.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057864 restraints weight = 115222.114| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6749 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= 0.155 Angle : 0.746 10.094 38466 Z= 0.382 Chirality : 0.048 0.267 4302 Planarity : 0.006 0.069 4950 Dihedral : 5.627 39.747 3762 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.38 % Favored : 91.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.14), residues: 3438 helix: -0.69 (0.13), residues: 1590 sheet: -1.29 (0.26), residues: 402 loop : -2.71 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F1162 HIS 0.011 0.002 HIS E 653 PHE 0.027 0.002 PHE E 741 TYR 0.035 0.002 TYR B 601 ARG 0.011 0.001 ARG D 354 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 1115) hydrogen bonds : angle 5.05709 ( 3306) covalent geometry : bond 0.00335 (28404) covalent geometry : angle 0.74595 (38466) ********************** 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 523 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 2.940 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: A 281 MET cc_start: 0.9183 (tpp) cc_final: 0.8729 (tpp) REVERT: A 334 TYR cc_start: 0.8275 (m-80) cc_final: 0.7944 (m-80) REVERT: A 371 ASP cc_start: 0.9660 (t0) cc_final: 0.9321 (m-30) REVERT: A 410 ILE cc_start: 0.9169 (pt) cc_final: 0.8966 (pt) REVERT: A 649 THR cc_start: 0.9656 (m) cc_final: 0.9260 (p) REVERT: A 653 HIS cc_start: 0.9522 (m-70) cc_final: 0.9261 (m-70) REVERT: A 673 ASN cc_start: 0.9550 (t0) cc_final: 0.9240 (t0) REVERT: A 689 MET cc_start: 0.9660 (tpp) cc_final: 0.9055 (tpp) REVERT: A 1152 HIS cc_start: 0.9771 (m90) cc_final: 0.9257 (m-70) REVERT: A 1157 LEU cc_start: 0.9500 (mm) cc_final: 0.9262 (pp) REVERT: B 288 TYR cc_start: 0.9407 (m-10) cc_final: 0.9196 (m-10) REVERT: B 320 LEU cc_start: 0.9367 (mt) cc_final: 0.9107 (mt) REVERT: B 411 ILE cc_start: 0.9667 (mp) cc_final: 0.9449 (mp) REVERT: B 469 GLU cc_start: 0.9685 (pt0) cc_final: 0.9469 (pt0) REVERT: B 521 MET cc_start: 0.9606 (mtm) cc_final: 0.9129 (mtp) REVERT: B 564 MET cc_start: 0.9138 (ttp) cc_final: 0.8905 (ppp) REVERT: B 595 PHE cc_start: 0.9312 (m-80) cc_final: 0.9045 (m-10) REVERT: B 636 MET cc_start: 0.9577 (mmt) cc_final: 0.9336 (mmp) REVERT: B 658 VAL cc_start: 0.9241 (m) cc_final: 0.8993 (m) REVERT: B 1185 MET cc_start: 0.8762 (mtt) cc_final: 0.8523 (mmm) REVERT: C 266 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8508 (tm-30) REVERT: C 320 LEU cc_start: 0.8741 (mt) cc_final: 0.8195 (mt) REVERT: C 350 GLU cc_start: 0.9346 (tp30) cc_final: 0.7966 (mp0) REVERT: C 480 ARG cc_start: 0.9680 (mmt90) cc_final: 0.9169 (mmm-85) REVERT: C 519 PHE cc_start: 0.9380 (m-80) cc_final: 0.9119 (m-80) REVERT: C 523 MET cc_start: 0.9482 (tpp) cc_final: 0.9178 (tpp) REVERT: C 592 LEU cc_start: 0.9551 (pt) cc_final: 0.9291 (pt) REVERT: C 636 MET cc_start: 0.9172 (pmm) cc_final: 0.8745 (pmm) REVERT: C 689 MET cc_start: 0.9490 (mmp) cc_final: 0.9244 (mmm) REVERT: C 1152 HIS cc_start: 0.9332 (m170) cc_final: 0.8905 (m-70) REVERT: D 283 MET cc_start: 0.8907 (ptt) cc_final: 0.8512 (ptt) REVERT: D 351 ARG cc_start: 0.9417 (mmm160) cc_final: 0.9173 (ttt180) REVERT: D 370 PHE cc_start: 0.9015 (m-80) cc_final: 0.8782 (m-80) REVERT: D 371 ASP cc_start: 0.9641 (m-30) cc_final: 0.9423 (p0) REVERT: D 591 ARG cc_start: 0.9292 (mtt90) cc_final: 0.9072 (mtt-85) REVERT: D 592 LEU cc_start: 0.9073 (mm) cc_final: 0.8727 (mm) REVERT: D 660 ARG cc_start: 0.9074 (ptt-90) cc_final: 0.8755 (ptt90) REVERT: E 328 ASN cc_start: 0.8647 (t0) cc_final: 0.8331 (p0) REVERT: E 642 ASP cc_start: 0.8158 (t70) cc_final: 0.7647 (t70) REVERT: E 701 PHE cc_start: 0.9683 (t80) cc_final: 0.8982 (t80) REVERT: F 370 PHE cc_start: 0.9148 (m-80) cc_final: 0.8847 (m-80) REVERT: F 451 HIS cc_start: 0.8986 (m-70) cc_final: 0.8585 (m-70) REVERT: F 592 LEU cc_start: 0.9654 (pt) cc_final: 0.9393 (pt) REVERT: F 601 TYR cc_start: 0.8427 (t80) cc_final: 0.8218 (t80) REVERT: F 645 GLN cc_start: 0.9499 (pt0) cc_final: 0.8900 (pt0) REVERT: F 653 HIS cc_start: 0.9506 (m90) cc_final: 0.9131 (m90) REVERT: F 657 GLU cc_start: 0.9554 (mp0) cc_final: 0.9214 (mp0) REVERT: F 689 MET cc_start: 0.9771 (mmm) cc_final: 0.9344 (mmm) REVERT: F 741 PHE cc_start: 0.9076 (m-80) cc_final: 0.8536 (m-10) REVERT: F 1156 PHE cc_start: 0.9686 (m-10) cc_final: 0.9435 (m-10) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.4207 time to fit residues: 338.2517 Evaluate side-chains 401 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 126 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 156 optimal weight: 0.0770 chunk 171 optimal weight: 0.9990 chunk 329 optimal weight: 5.9990 chunk 333 optimal weight: 2.9990 chunk 236 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 234 optimal weight: 20.0000 overall best weight: 1.4144 ------------------------------------------------------------------------------- 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 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 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 653 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.083584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.059123 restraints weight = 175130.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.060436 restraints weight = 132388.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061418 restraints weight = 107592.339| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.6920 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= 0.125 Angle : 0.730 9.760 38466 Z= 0.369 Chirality : 0.048 0.258 4302 Planarity : 0.006 0.070 4950 Dihedral : 5.509 39.915 3762 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.14), residues: 3438 helix: -0.56 (0.13), residues: 1620 sheet: -1.23 (0.26), residues: 402 loop : -2.70 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 674 HIS 0.008 0.001 HIS F 661 PHE 0.016 0.001 PHE B 553 TYR 0.029 0.001 TYR B1158 ARG 0.011 0.001 ARG C 493 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 1115) hydrogen bonds : angle 4.90751 ( 3306) covalent geometry : bond 0.00271 (28404) covalent geometry : angle 0.72970 (38466) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10802.83 seconds wall clock time: 190 minutes 46.61 seconds (11446.61 seconds total)