Starting phenix.real_space_refine on Sun Aug 24 12:37:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sl8_40575/08_2025/8sl8_40575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sl8_40575/08_2025/8sl8_40575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sl8_40575/08_2025/8sl8_40575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sl8_40575/08_2025/8sl8_40575.map" model { file = "/net/cci-nas-00/data/ceres_data/8sl8_40575/08_2025/8sl8_40575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sl8_40575/08_2025/8sl8_40575.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.022 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 48 5.16 5 C 12460 2.51 5 N 3516 2.21 5 O 3664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19688 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 4922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 4922 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 393} Link IDs: {'PTRANS': 28, 'TRANS': 759} Chain breaks: 14 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1547 Unresolved non-hydrogen angles: 1961 Unresolved non-hydrogen dihedrals: 1298 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'PHE:plan': 27, 'GLU:plan': 40, 'TRP:plan': 7, 'HIS:plan': 12, 'ARG:plan': 35, 'ASP:plan': 23, 'GLN:plan1': 22, 'ASN:plan1': 8, 'TYR:plan': 11} Unresolved non-hydrogen planarities: 878 Restraints were copied for chains: A, C, D Time building chain proxies: 4.78, per 1000 atoms: 0.24 Number of scatterers: 19688 At special positions: 0 Unit cell: (141.48, 141.48, 155.52, 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 48 16.00 O 3664 8.00 N 3516 7.00 C 12460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6032 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 4 sheets defined 79.3% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'B' and resid 48 through 58 removed outlier: 3.719A pdb=" N LEU B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 262 through 272 removed outlier: 4.003A pdb=" N GLY B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 329 through 345 removed outlier: 3.785A pdb=" N HIS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 345 " --> pdb=" O CYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 362 removed outlier: 3.892A pdb=" N ASP B 353 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'B' and resid 379 through 393 removed outlier: 3.599A pdb=" N LEU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU B 385 " --> pdb=" O CYS B 381 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 405 removed outlier: 4.028A pdb=" N VAL B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 414 through 424 Processing helix chain 'B' and resid 429 through 446 Processing helix chain 'B' and resid 465 through 478 Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.501A pdb=" N ASP B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 removed outlier: 3.511A pdb=" N MET B 539 " --> pdb=" O TYR B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 561 removed outlier: 3.540A pdb=" N ALA B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS B 559 " --> pdb=" O LYS B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 571 Processing helix chain 'B' and resid 574 through 590 removed outlier: 3.885A pdb=" N LEU B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 599 Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 609 through 618 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'B' and resid 645 through 655 removed outlier: 3.912A pdb=" N CYS B 655 " --> pdb=" O GLY B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 662 Processing helix chain 'B' and resid 719 through 727 Processing helix chain 'B' and resid 729 through 757 removed outlier: 3.810A pdb=" N LEU B 753 " --> pdb=" O SER B 749 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL B 754 " --> pdb=" O TYR B 750 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 786 removed outlier: 4.563A pdb=" N PHE B 775 " --> pdb=" O TYR B 771 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N THR B 776 " --> pdb=" O PHE B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 826 removed outlier: 3.586A pdb=" N PHE B 817 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 818 " --> pdb=" O ILE B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 851 removed outlier: 4.283A pdb=" N LEU B 837 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE B 844 " --> pdb=" O ASP B 840 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR B 845 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS B 850 " --> pdb=" O LEU B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 868 removed outlier: 4.483A pdb=" N LYS B 861 " --> pdb=" O GLN B 857 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 863 " --> pdb=" O GLY B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 895 removed outlier: 3.687A pdb=" N PHE B 875 " --> pdb=" O ASP B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 917 removed outlier: 4.824A pdb=" N ARG B 911 " --> pdb=" O ARG B 907 " (cutoff:3.500A) Proline residue: B 912 - end of helix Processing helix chain 'B' and resid 921 through 926 Processing helix chain 'B' and resid 959 through 1006 removed outlier: 3.537A pdb=" N PHE B 977 " --> pdb=" O LEU B 973 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 981 " --> pdb=" O PHE B 977 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLN B 982 " --> pdb=" O SER B 978 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 983 " --> pdb=" O TYR B 979 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY B 986 " --> pdb=" O GLN B 982 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET B 990 " --> pdb=" O GLY B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1027 removed outlier: 3.748A pdb=" N LEU B1015 " --> pdb=" O PRO B1011 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1071 Processing helix chain 'B' and resid 1072 through 1092 Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.719A pdb=" N LEU A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 239 through 249 Processing helix chain 'A' and resid 262 through 272 removed outlier: 4.003A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 329 through 345 removed outlier: 3.785A pdb=" N HIS A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 345 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 removed outlier: 3.892A pdb=" N ASP A 353 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'A' and resid 379 through 393 removed outlier: 3.598A pdb=" N LEU A 383 " --> pdb=" O LYS A 379 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU A 385 " --> pdb=" O CYS A 381 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 removed outlier: 4.028A pdb=" N VAL A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 429 through 446 Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.501A pdb=" N ASP A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.512A pdb=" N MET A 539 " --> pdb=" O TYR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 561 removed outlier: 3.540A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 Processing helix chain 'A' and resid 574 through 590 removed outlier: 3.885A pdb=" N LEU A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 602 through 606 Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'A' and resid 645 through 655 removed outlier: 3.912A pdb=" N CYS A 655 " --> pdb=" O GLY A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 719 through 727 Processing helix chain 'A' and resid 729 through 757 removed outlier: 3.810A pdb=" N LEU A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 754 " --> pdb=" O TYR A 750 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 786 removed outlier: 4.564A pdb=" N PHE A 775 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N THR A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 826 removed outlier: 3.586A pdb=" N PHE A 817 " --> pdb=" O ALA A 813 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 851 removed outlier: 4.283A pdb=" N LEU A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE A 844 " --> pdb=" O ASP A 840 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR A 845 " --> pdb=" O PHE A 841 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 868 removed outlier: 4.483A pdb=" N LYS A 861 " --> pdb=" O GLN A 857 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 863 " --> pdb=" O GLY A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 895 removed outlier: 3.687A pdb=" N PHE A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 917 removed outlier: 4.824A pdb=" N ARG A 911 " --> pdb=" O ARG A 907 " (cutoff:3.500A) Proline residue: A 912 - end of helix Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'A' and resid 959 through 1006 removed outlier: 3.537A pdb=" N PHE A 977 " --> pdb=" O LEU A 973 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 981 " --> pdb=" O PHE A 977 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLN A 982 " --> pdb=" O SER A 978 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 983 " --> pdb=" O TYR A 979 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 984 " --> pdb=" O THR A 980 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY A 986 " --> pdb=" O GLN A 982 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 990 " --> pdb=" O GLY A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1027 removed outlier: 3.748A pdb=" N LEU A1015 " --> pdb=" O PRO A1011 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A1016 " --> pdb=" O PRO A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1071 Processing helix chain 'A' and resid 1072 through 1092 Processing helix chain 'C' and resid 48 through 58 removed outlier: 3.719A pdb=" N LEU C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 201 through 214 Processing helix chain 'C' and resid 239 through 249 Processing helix chain 'C' and resid 262 through 272 removed outlier: 4.003A pdb=" N GLY C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 289 Processing helix chain 'C' and resid 296 through 310 Processing helix chain 'C' and resid 329 through 345 removed outlier: 3.785A pdb=" N HIS C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 345 " --> pdb=" O CYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 362 removed outlier: 3.892A pdb=" N ASP C 353 " --> pdb=" O GLN C 349 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU C 354 " --> pdb=" O ASP C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 379 through 393 removed outlier: 3.599A pdb=" N LEU C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU C 385 " --> pdb=" O CYS C 381 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 405 removed outlier: 4.029A pdb=" N VAL C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 414 through 424 Processing helix chain 'C' and resid 429 through 446 Processing helix chain 'C' and resid 465 through 478 Processing helix chain 'C' and resid 515 through 527 removed outlier: 3.501A pdb=" N ASP C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 539 removed outlier: 3.511A pdb=" N MET C 539 " --> pdb=" O TYR C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 561 removed outlier: 3.540A pdb=" N ALA C 546 " --> pdb=" O GLU C 542 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS C 559 " --> pdb=" O LYS C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 571 Processing helix chain 'C' and resid 574 through 590 removed outlier: 3.885A pdb=" N LEU C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 599 Processing helix chain 'C' and resid 602 through 606 Processing helix chain 'C' and resid 609 through 618 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 625 through 637 Processing helix chain 'C' and resid 645 through 655 removed outlier: 3.912A pdb=" N CYS C 655 " --> pdb=" O GLY C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 662 Processing helix chain 'C' and resid 719 through 727 Processing helix chain 'C' and resid 729 through 757 removed outlier: 3.810A pdb=" N LEU C 753 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL C 754 " --> pdb=" O TYR C 750 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 786 removed outlier: 4.563A pdb=" N PHE C 775 " --> pdb=" O TYR C 771 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR C 776 " --> pdb=" O PHE C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 826 removed outlier: 3.586A pdb=" N PHE C 817 " --> pdb=" O ALA C 813 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 818 " --> pdb=" O ILE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 851 removed outlier: 4.284A pdb=" N LEU C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE C 844 " --> pdb=" O ASP C 840 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR C 845 " --> pdb=" O PHE C 841 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS C 850 " --> pdb=" O LEU C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 868 removed outlier: 4.482A pdb=" N LYS C 861 " --> pdb=" O GLN C 857 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 863 " --> pdb=" O GLY C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 895 removed outlier: 3.688A pdb=" N PHE C 875 " --> pdb=" O ASP C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 917 removed outlier: 4.823A pdb=" N ARG C 911 " --> pdb=" O ARG C 907 " (cutoff:3.500A) Proline residue: C 912 - end of helix Processing helix chain 'C' and resid 921 through 926 Processing helix chain 'C' and resid 959 through 1006 removed outlier: 3.537A pdb=" N PHE C 977 " --> pdb=" O LEU C 973 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 981 " --> pdb=" O PHE C 977 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLN C 982 " --> pdb=" O SER C 978 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL C 983 " --> pdb=" O TYR C 979 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL C 984 " --> pdb=" O THR C 980 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY C 986 " --> pdb=" O GLN C 982 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET C 990 " --> pdb=" O GLY C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1027 removed outlier: 3.749A pdb=" N LEU C1015 " --> pdb=" O PRO C1011 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU C1016 " --> pdb=" O PRO C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1044 through 1071 Processing helix chain 'C' and resid 1072 through 1092 Processing helix chain 'D' and resid 48 through 58 removed outlier: 3.719A pdb=" N LEU D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 97 Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 201 through 214 Processing helix chain 'D' and resid 239 through 249 Processing helix chain 'D' and resid 262 through 272 removed outlier: 4.003A pdb=" N GLY D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 289 Processing helix chain 'D' and resid 296 through 310 Processing helix chain 'D' and resid 329 through 345 removed outlier: 3.784A pdb=" N HIS D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 345 " --> pdb=" O CYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 362 removed outlier: 3.892A pdb=" N ASP D 353 " --> pdb=" O GLN D 349 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU D 354 " --> pdb=" O ASP D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 379 through 393 removed outlier: 3.599A pdb=" N LEU D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU D 385 " --> pdb=" O CYS D 381 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 405 removed outlier: 4.028A pdb=" N VAL D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 414 through 424 Processing helix chain 'D' and resid 429 through 446 Processing helix chain 'D' and resid 465 through 478 Processing helix chain 'D' and resid 515 through 527 removed outlier: 3.500A pdb=" N ASP D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.511A pdb=" N MET D 539 " --> pdb=" O TYR D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 561 removed outlier: 3.540A pdb=" N ALA D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS D 559 " --> pdb=" O LYS D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 571 Processing helix chain 'D' and resid 574 through 590 removed outlier: 3.885A pdb=" N LEU D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 599 Processing helix chain 'D' and resid 602 through 606 Processing helix chain 'D' and resid 609 through 618 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 645 through 655 removed outlier: 3.911A pdb=" N CYS D 655 " --> pdb=" O GLY D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 662 Processing helix chain 'D' and resid 719 through 727 Processing helix chain 'D' and resid 729 through 757 removed outlier: 3.811A pdb=" N LEU D 753 " --> pdb=" O SER D 749 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL D 754 " --> pdb=" O TYR D 750 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG D 757 " --> pdb=" O LEU D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 786 removed outlier: 4.564A pdb=" N PHE D 775 " --> pdb=" O TYR D 771 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N THR D 776 " --> pdb=" O PHE D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 826 removed outlier: 3.586A pdb=" N PHE D 817 " --> pdb=" O ALA D 813 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 818 " --> pdb=" O ILE D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 851 removed outlier: 4.284A pdb=" N LEU D 837 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET D 842 " --> pdb=" O ALA D 838 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL D 843 " --> pdb=" O ILE D 839 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE D 844 " --> pdb=" O ASP D 840 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR D 845 " --> pdb=" O PHE D 841 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS D 850 " --> pdb=" O LEU D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 868 removed outlier: 4.483A pdb=" N LYS D 861 " --> pdb=" O GLN D 857 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 863 " --> pdb=" O GLY D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 895 removed outlier: 3.687A pdb=" N PHE D 875 " --> pdb=" O ASP D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 917 removed outlier: 4.824A pdb=" N ARG D 911 " --> pdb=" O ARG D 907 " (cutoff:3.500A) Proline residue: D 912 - end of helix Processing helix chain 'D' and resid 921 through 926 Processing helix chain 'D' and resid 959 through 1006 removed outlier: 3.537A pdb=" N PHE D 977 " --> pdb=" O LEU D 973 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 981 " --> pdb=" O PHE D 977 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLN D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL D 983 " --> pdb=" O TYR D 979 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 984 " --> pdb=" O THR D 980 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY D 986 " --> pdb=" O GLN D 982 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET D 990 " --> pdb=" O GLY D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1027 removed outlier: 3.748A pdb=" N LEU D1015 " --> pdb=" O PRO D1011 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU D1016 " --> pdb=" O PRO D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1044 through 1071 Processing helix chain 'D' and resid 1072 through 1092 Processing sheet with id=AA1, first strand: chain 'B' and resid 103 through 104 removed outlier: 6.126A pdb=" N VAL B 69 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 317 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104 removed outlier: 6.126A pdb=" N VAL A 69 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 317 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 103 through 104 removed outlier: 6.127A pdb=" N VAL C 69 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 317 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 103 through 104 removed outlier: 6.126A pdb=" N VAL D 69 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 317 " --> pdb=" O TRP D 253 " (cutoff:3.500A) 1656 hydrogen bonds defined for protein. 4944 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: 4.02 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6790 1.34 - 1.46: 3551 1.46 - 1.57: 9611 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 20024 Sorted by residual: bond pdb=" CG1 ILE A 554 " pdb=" CD1 ILE A 554 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.83e+00 bond pdb=" CG1 ILE C 554 " pdb=" CD1 ILE C 554 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.81e+00 bond pdb=" CG1 ILE D 554 " pdb=" CD1 ILE D 554 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.81e+00 bond pdb=" CG1 ILE B 554 " pdb=" CD1 ILE B 554 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.81e+00 bond pdb=" CB ILE B 554 " pdb=" CG2 ILE B 554 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.41e+00 ... (remaining 20019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 26570 1.51 - 3.03: 910 3.03 - 4.54: 78 4.54 - 6.06: 58 6.06 - 7.57: 16 Bond angle restraints: 27632 Sorted by residual: angle pdb=" N ALA C 641 " pdb=" CA ALA C 641 " pdb=" C ALA C 641 " ideal model delta sigma weight residual 111.28 116.82 -5.54 1.09e+00 8.42e-01 2.58e+01 angle pdb=" N ALA B 641 " pdb=" CA ALA B 641 " pdb=" C ALA B 641 " ideal model delta sigma weight residual 111.28 116.80 -5.52 1.09e+00 8.42e-01 2.56e+01 angle pdb=" N ALA A 641 " pdb=" CA ALA A 641 " pdb=" C ALA A 641 " ideal model delta sigma weight residual 111.28 116.79 -5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" C LEU B 229 " pdb=" N CYS B 230 " pdb=" CA CYS B 230 " ideal model delta sigma weight residual 122.94 115.37 7.57 1.50e+00 4.44e-01 2.55e+01 angle pdb=" C LEU C 229 " pdb=" N CYS C 230 " pdb=" CA CYS C 230 " ideal model delta sigma weight residual 122.94 115.37 7.57 1.50e+00 4.44e-01 2.55e+01 ... (remaining 27627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 10808 15.04 - 30.08: 504 30.08 - 45.13: 140 45.13 - 60.17: 28 60.17 - 75.21: 12 Dihedral angle restraints: 11492 sinusoidal: 2336 harmonic: 9156 Sorted by residual: dihedral pdb=" CA GLU A 377 " pdb=" C GLU A 377 " pdb=" N TRP A 378 " pdb=" CA TRP A 378 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA GLU D 377 " pdb=" C GLU D 377 " pdb=" N TRP D 378 " pdb=" CA TRP D 378 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA GLU B 377 " pdb=" C GLU B 377 " pdb=" N TRP B 378 " pdb=" CA TRP B 378 " ideal model delta harmonic sigma weight residual -180.00 -158.16 -21.84 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 11489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3311 0.076 - 0.152: 155 0.152 - 0.229: 6 0.229 - 0.305: 8 0.305 - 0.381: 4 Chirality restraints: 3484 Sorted by residual: chirality pdb=" CB ILE D 554 " pdb=" CA ILE D 554 " pdb=" CG1 ILE D 554 " pdb=" CG2 ILE D 554 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB ILE B 554 " pdb=" CA ILE B 554 " pdb=" CG1 ILE B 554 " pdb=" CG2 ILE B 554 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE C 554 " pdb=" CA ILE C 554 " pdb=" CG1 ILE C 554 " pdb=" CG2 ILE C 554 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 3481 not shown) Planarity restraints: 3636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 570 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C MET A 570 " 0.030 2.00e-02 2.50e+03 pdb=" O MET A 570 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 571 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 570 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C MET B 570 " 0.029 2.00e-02 2.50e+03 pdb=" O MET B 570 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG B 571 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 570 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C MET C 570 " -0.029 2.00e-02 2.50e+03 pdb=" O MET C 570 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG C 571 " 0.010 2.00e-02 2.50e+03 ... (remaining 3633 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2293 2.74 - 3.28: 22208 3.28 - 3.82: 33919 3.82 - 4.36: 32984 4.36 - 4.90: 56147 Nonbonded interactions: 147551 Sorted by model distance: nonbonded pdb=" O GLU A 385 " pdb=" OG1 THR A 388 " model vdw 2.201 3.040 nonbonded pdb=" O GLU B 385 " pdb=" OG1 THR B 388 " model vdw 2.202 3.040 nonbonded pdb=" O GLU C 385 " pdb=" OG1 THR C 388 " model vdw 2.202 3.040 nonbonded pdb=" O GLU D 385 " pdb=" OG1 THR D 388 " model vdw 2.202 3.040 nonbonded pdb=" N VAL A 68 " pdb=" O PRO A 227 " model vdw 2.212 3.120 ... (remaining 147546 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.840 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.004 0.066 20024 Z= 0.204 Angle : 0.678 7.570 27632 Z= 0.451 Chirality : 0.041 0.381 3484 Planarity : 0.003 0.034 3636 Dihedral : 10.975 75.209 5460 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.14), residues: 3032 helix: -0.16 (0.10), residues: 2316 sheet: 0.41 (0.58), residues: 84 loop : -1.89 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.010 0.001 TYR D 535 PHE 0.014 0.001 PHE C 994 TRP 0.012 0.001 TRP B 636 HIS 0.005 0.001 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00365 (20024) covalent geometry : angle 0.67758 (27632) hydrogen bonds : bond 0.13659 ( 1656) hydrogen bonds : angle 5.87416 ( 4944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 773 TRP cc_start: 0.7613 (m100) cc_final: 0.6918 (m100) REVERT: B 882 TRP cc_start: 0.9269 (t-100) cc_final: 0.9051 (t-100) REVERT: B 1050 ILE cc_start: 0.9615 (mt) cc_final: 0.9382 (tp) REVERT: B 1057 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8379 (tp40) REVERT: A 398 PHE cc_start: 0.8067 (m-80) cc_final: 0.7864 (m-80) REVERT: A 409 MET cc_start: 0.8650 (mmm) cc_final: 0.8428 (mmp) REVERT: A 420 GLN cc_start: 0.8872 (tt0) cc_final: 0.8310 (tp-100) REVERT: A 773 TRP cc_start: 0.7624 (m100) cc_final: 0.6705 (m100) REVERT: A 1050 ILE cc_start: 0.9593 (mt) cc_final: 0.9323 (tp) REVERT: A 1057 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8401 (tp40) REVERT: C 773 TRP cc_start: 0.7538 (m100) cc_final: 0.6735 (m100) REVERT: C 1050 ILE cc_start: 0.9590 (mt) cc_final: 0.9318 (tp) REVERT: C 1057 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8510 (tp40) REVERT: D 773 TRP cc_start: 0.7450 (m100) cc_final: 0.6597 (m100) REVERT: D 845 THR cc_start: 0.9495 (p) cc_final: 0.9290 (p) REVERT: D 1050 ILE cc_start: 0.9604 (mt) cc_final: 0.9309 (tp) REVERT: D 1057 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8507 (tp40) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1097 time to fit residues: 36.1206 Evaluate side-chains 149 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 50.0000 overall best weight: 4.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 528 ASN B 602 ASN ** B1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 602 ASN C 528 ASN C 602 ASN C1048 GLN ** C1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 528 ASN D 602 ASN ** D1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.069980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.051822 restraints weight = 160862.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.052971 restraints weight = 97391.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.053689 restraints weight = 70514.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.054121 restraints weight = 57384.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.054397 restraints weight = 50552.515| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20024 Z= 0.235 Angle : 0.591 6.685 27632 Z= 0.331 Chirality : 0.039 0.238 3484 Planarity : 0.004 0.041 3636 Dihedral : 4.395 26.296 3172 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.93 % Allowed : 8.05 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.15), residues: 3032 helix: 1.48 (0.10), residues: 2356 sheet: 0.06 (0.57), residues: 84 loop : -1.44 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 518 TYR 0.023 0.002 TYR D 535 PHE 0.022 0.002 PHE B 631 TRP 0.014 0.002 TRP C 882 HIS 0.006 0.002 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00452 (20024) covalent geometry : angle 0.59070 (27632) hydrogen bonds : bond 0.03650 ( 1656) hydrogen bonds : angle 4.43983 ( 4944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: B 773 TRP cc_start: 0.8421 (m100) cc_final: 0.7692 (m100) REVERT: A 1057 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8299 (mm-40) REVERT: C 773 TRP cc_start: 0.8430 (m100) cc_final: 0.7502 (m100) REVERT: C 842 MET cc_start: 0.8757 (mmp) cc_final: 0.8454 (mmp) REVERT: C 1057 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8336 (mm-40) REVERT: D 1057 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8339 (tp40) outliers start: 11 outliers final: 3 residues processed: 184 average time/residue: 0.1111 time to fit residues: 35.6814 Evaluate side-chains 141 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 260 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 185 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 95 optimal weight: 30.0000 chunk 138 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 16 optimal weight: 40.0000 overall best weight: 6.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 528 ASN B 612 HIS ** B1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 612 HIS ** A1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN C 612 HIS ** C1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 HIS ** D1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.068531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.050491 restraints weight = 163910.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.051644 restraints weight = 98264.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.052360 restraints weight = 70833.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.052790 restraints weight = 57715.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.053064 restraints weight = 50860.406| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20024 Z= 0.309 Angle : 0.669 11.059 27632 Z= 0.374 Chirality : 0.041 0.204 3484 Planarity : 0.004 0.038 3636 Dihedral : 4.723 27.031 3172 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.25 % Allowed : 6.69 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.15), residues: 3032 helix: 1.49 (0.10), residues: 2332 sheet: 0.07 (0.65), residues: 84 loop : -1.51 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 518 TYR 0.025 0.002 TYR A 535 PHE 0.026 0.002 PHE D 631 TRP 0.019 0.002 TRP A 361 HIS 0.006 0.002 HIS D 998 Details of bonding type rmsd covalent geometry : bond 0.00584 (20024) covalent geometry : angle 0.66859 (27632) hydrogen bonds : bond 0.04208 ( 1656) hydrogen bonds : angle 4.78071 ( 4944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 398 PHE cc_start: 0.8420 (m-80) cc_final: 0.8067 (m-80) REVERT: C 398 PHE cc_start: 0.8425 (m-80) cc_final: 0.8125 (m-80) REVERT: D 398 PHE cc_start: 0.8459 (m-80) cc_final: 0.8185 (m-80) outliers start: 3 outliers final: 0 residues processed: 153 average time/residue: 0.1091 time to fit residues: 30.0817 Evaluate side-chains 124 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 172 optimal weight: 50.0000 chunk 117 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 chunk 281 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 283 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 269 optimal weight: 4.9990 chunk 306 optimal weight: 0.2980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.071727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.053494 restraints weight = 159715.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.054698 restraints weight = 95971.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.055465 restraints weight = 69033.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.055967 restraints weight = 55652.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.056267 restraints weight = 48540.432| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20024 Z= 0.105 Angle : 0.481 6.443 27632 Z= 0.256 Chirality : 0.036 0.141 3484 Planarity : 0.003 0.035 3636 Dihedral : 4.018 23.339 3172 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.25 % Allowed : 1.61 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.15), residues: 3032 helix: 2.22 (0.10), residues: 2356 sheet: 0.27 (0.65), residues: 84 loop : -1.42 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 518 TYR 0.011 0.001 TYR B 535 PHE 0.016 0.001 PHE C 476 TRP 0.014 0.002 TRP D 523 HIS 0.004 0.001 HIS C 998 Details of bonding type rmsd covalent geometry : bond 0.00209 (20024) covalent geometry : angle 0.48058 (27632) hydrogen bonds : bond 0.02928 ( 1656) hydrogen bonds : angle 3.74482 ( 4944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 422 TYR cc_start: 0.8386 (m-80) cc_final: 0.7153 (m-80) REVERT: B 842 MET cc_start: 0.8921 (mmp) cc_final: 0.8644 (mmp) REVERT: A 422 TYR cc_start: 0.8550 (m-80) cc_final: 0.8203 (m-80) REVERT: A 1057 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8283 (tp40) REVERT: C 422 TYR cc_start: 0.8460 (m-80) cc_final: 0.7222 (m-80) REVERT: C 1057 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8263 (tp40) REVERT: D 422 TYR cc_start: 0.8486 (m-80) cc_final: 0.8203 (m-80) REVERT: D 1057 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8319 (tp40) outliers start: 3 outliers final: 3 residues processed: 179 average time/residue: 0.1067 time to fit residues: 33.8104 Evaluate side-chains 150 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 258 optimal weight: 3.9990 chunk 224 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 chunk 278 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 233 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1060 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.070481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.052235 restraints weight = 159780.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.053436 restraints weight = 96047.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.054172 restraints weight = 69111.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.054661 restraints weight = 56007.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.054914 restraints weight = 49121.355| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20024 Z= 0.167 Angle : 0.507 6.545 27632 Z= 0.279 Chirality : 0.036 0.159 3484 Planarity : 0.003 0.036 3636 Dihedral : 4.031 23.573 3172 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.15), residues: 3032 helix: 2.38 (0.10), residues: 2352 sheet: 0.27 (0.66), residues: 84 loop : -1.51 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 518 TYR 0.019 0.002 TYR B 535 PHE 0.017 0.002 PHE A 631 TRP 0.011 0.001 TRP D 378 HIS 0.006 0.001 HIS C 612 Details of bonding type rmsd covalent geometry : bond 0.00326 (20024) covalent geometry : angle 0.50663 (27632) hydrogen bonds : bond 0.03052 ( 1656) hydrogen bonds : angle 3.88815 ( 4944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 1057 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8304 (tp40) REVERT: C 1057 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8430 (tp40) REVERT: D 422 TYR cc_start: 0.8391 (m-80) cc_final: 0.8052 (m-80) REVERT: D 1057 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8338 (tp40) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1087 time to fit residues: 32.5175 Evaluate side-chains 146 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 111 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 61 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 244 optimal weight: 20.0000 chunk 84 optimal weight: 50.0000 chunk 30 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.071828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.053570 restraints weight = 157673.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.054791 restraints weight = 95088.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.055551 restraints weight = 68352.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.056009 restraints weight = 55436.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.056250 restraints weight = 48686.579| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20024 Z= 0.108 Angle : 0.463 6.472 27632 Z= 0.246 Chirality : 0.035 0.132 3484 Planarity : 0.003 0.036 3636 Dihedral : 3.758 21.903 3172 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.16), residues: 3032 helix: 2.60 (0.10), residues: 2364 sheet: 0.29 (0.66), residues: 84 loop : -1.45 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.011 0.001 TYR B 535 PHE 0.009 0.001 PHE B 631 TRP 0.013 0.001 TRP D 636 HIS 0.003 0.001 HIS C 612 Details of bonding type rmsd covalent geometry : bond 0.00220 (20024) covalent geometry : angle 0.46268 (27632) hydrogen bonds : bond 0.02613 ( 1656) hydrogen bonds : angle 3.58885 ( 4944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.820 Fit side-chains REVERT: B 422 TYR cc_start: 0.8382 (m-80) cc_final: 0.7148 (m-80) REVERT: B 842 MET cc_start: 0.8915 (mmp) cc_final: 0.8631 (mmp) REVERT: A 422 TYR cc_start: 0.8622 (m-80) cc_final: 0.8233 (m-80) REVERT: A 1057 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8367 (tp40) REVERT: C 422 TYR cc_start: 0.8387 (m-80) cc_final: 0.7186 (m-80) REVERT: C 842 MET cc_start: 0.8732 (mmp) cc_final: 0.8445 (mmp) REVERT: C 1057 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8471 (tp40) REVERT: D 422 TYR cc_start: 0.8504 (m-80) cc_final: 0.8187 (m-80) REVERT: D 634 LYS cc_start: 0.9329 (tmtt) cc_final: 0.9123 (tptp) REVERT: D 1057 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8437 (tp40) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1099 time to fit residues: 33.5351 Evaluate side-chains 147 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 244 optimal weight: 30.0000 chunk 235 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 252 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 chunk 188 optimal weight: 10.0000 overall best weight: 4.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1060 ASN ** C1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.069867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.051633 restraints weight = 160610.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.052833 restraints weight = 95841.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.053571 restraints weight = 68636.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.054034 restraints weight = 55582.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.054282 restraints weight = 48738.659| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20024 Z= 0.201 Angle : 0.550 6.687 27632 Z= 0.301 Chirality : 0.037 0.139 3484 Planarity : 0.004 0.036 3636 Dihedral : 4.078 23.901 3172 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.16), residues: 3032 helix: 2.37 (0.11), residues: 2356 sheet: 0.02 (0.66), residues: 84 loop : -1.46 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 518 TYR 0.023 0.002 TYR B 535 PHE 0.020 0.002 PHE B 631 TRP 0.016 0.002 TRP A 523 HIS 0.009 0.001 HIS C 612 Details of bonding type rmsd covalent geometry : bond 0.00389 (20024) covalent geometry : angle 0.54978 (27632) hydrogen bonds : bond 0.03195 ( 1656) hydrogen bonds : angle 4.01870 ( 4944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.967 Fit side-chains REVERT: A 398 PHE cc_start: 0.8746 (m-80) cc_final: 0.8420 (m-80) REVERT: C 398 PHE cc_start: 0.8694 (m-80) cc_final: 0.8455 (m-80) REVERT: D 634 LYS cc_start: 0.9352 (tmtt) cc_final: 0.9107 (tptp) REVERT: D 1057 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8644 (tp40) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1055 time to fit residues: 30.4439 Evaluate side-chains 141 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 311 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1060 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.070817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.052562 restraints weight = 158568.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.053773 restraints weight = 95120.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.054536 restraints weight = 68181.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.054939 restraints weight = 55160.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.055276 restraints weight = 48749.493| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20024 Z= 0.136 Angle : 0.498 7.123 27632 Z= 0.263 Chirality : 0.035 0.123 3484 Planarity : 0.003 0.037 3636 Dihedral : 3.876 22.353 3172 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.16), residues: 3032 helix: 2.57 (0.11), residues: 2360 sheet: -0.09 (0.66), residues: 84 loop : -1.47 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 518 TYR 0.015 0.001 TYR C 535 PHE 0.012 0.001 PHE B 631 TRP 0.014 0.001 TRP C 882 HIS 0.004 0.001 HIS D 612 Details of bonding type rmsd covalent geometry : bond 0.00270 (20024) covalent geometry : angle 0.49835 (27632) hydrogen bonds : bond 0.02754 ( 1656) hydrogen bonds : angle 3.71947 ( 4944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.818 Fit side-chains REVERT: A 398 PHE cc_start: 0.8602 (m-80) cc_final: 0.8179 (m-10) REVERT: A 1057 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8786 (tp40) REVERT: C 1057 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8814 (tp40) REVERT: D 422 TYR cc_start: 0.8717 (m-80) cc_final: 0.8320 (m-80) REVERT: D 634 LYS cc_start: 0.9341 (tmtt) cc_final: 0.9137 (tptp) REVERT: D 1057 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8639 (tp40) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1117 time to fit residues: 32.8244 Evaluate side-chains 138 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 49 optimal weight: 0.0270 chunk 202 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 chunk 183 optimal weight: 0.5980 chunk 280 optimal weight: 8.9990 overall best weight: 1.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.071563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.053302 restraints weight = 157204.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.054510 restraints weight = 93937.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.055277 restraints weight = 67581.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.055756 restraints weight = 54844.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.055995 restraints weight = 48062.604| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20024 Z= 0.110 Angle : 0.480 7.648 27632 Z= 0.250 Chirality : 0.035 0.126 3484 Planarity : 0.003 0.037 3636 Dihedral : 3.691 21.728 3172 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.89 (0.16), residues: 3032 helix: 2.75 (0.11), residues: 2360 sheet: -0.16 (0.65), residues: 84 loop : -1.50 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.012 0.001 TYR B 535 PHE 0.018 0.001 PHE D 744 TRP 0.025 0.001 TRP D 773 HIS 0.003 0.001 HIS C 612 Details of bonding type rmsd covalent geometry : bond 0.00223 (20024) covalent geometry : angle 0.47965 (27632) hydrogen bonds : bond 0.02582 ( 1656) hydrogen bonds : angle 3.53437 ( 4944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.731 Fit side-chains REVERT: B 398 PHE cc_start: 0.8239 (m-80) cc_final: 0.7876 (m-80) REVERT: B 422 TYR cc_start: 0.8339 (m-80) cc_final: 0.7118 (m-80) REVERT: A 398 PHE cc_start: 0.8227 (m-80) cc_final: 0.7827 (m-10) REVERT: D 634 LYS cc_start: 0.9288 (tmtt) cc_final: 0.9075 (tptp) REVERT: D 1057 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8434 (tp40) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1149 time to fit residues: 34.2276 Evaluate side-chains 134 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 206 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 266 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.071678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.053384 restraints weight = 157449.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.054602 restraints weight = 94853.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.055367 restraints weight = 68308.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.055843 restraints weight = 55268.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.056145 restraints weight = 48489.865| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20024 Z= 0.109 Angle : 0.492 8.939 27632 Z= 0.254 Chirality : 0.035 0.125 3484 Planarity : 0.003 0.037 3636 Dihedral : 3.588 21.109 3172 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.16), residues: 3032 helix: 2.78 (0.11), residues: 2364 sheet: -0.18 (0.65), residues: 84 loop : -1.50 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.016 0.001 TYR A 587 PHE 0.013 0.001 PHE D 744 TRP 0.025 0.001 TRP D 773 HIS 0.003 0.001 HIS C 612 Details of bonding type rmsd covalent geometry : bond 0.00219 (20024) covalent geometry : angle 0.49165 (27632) hydrogen bonds : bond 0.02533 ( 1656) hydrogen bonds : angle 3.54015 ( 4944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.817 Fit side-chains REVERT: B 398 PHE cc_start: 0.8590 (m-80) cc_final: 0.8187 (m-80) REVERT: A 398 PHE cc_start: 0.8581 (m-80) cc_final: 0.8120 (m-10) REVERT: D 634 LYS cc_start: 0.9335 (tmtt) cc_final: 0.9108 (tptp) REVERT: D 1057 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8684 (tp40) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1074 time to fit residues: 32.0437 Evaluate side-chains 135 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 87 optimal weight: 30.0000 chunk 165 optimal weight: 30.0000 chunk 88 optimal weight: 9.9990 chunk 275 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 chunk 175 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 HIS A1060 ASN C 423 HIS ** C1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 HIS ** D1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.069522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.051300 restraints weight = 161740.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.052488 restraints weight = 96432.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.053238 restraints weight = 69106.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.053710 restraints weight = 56013.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.053966 restraints weight = 49198.532| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20024 Z= 0.227 Angle : 0.591 7.974 27632 Z= 0.320 Chirality : 0.037 0.122 3484 Planarity : 0.004 0.038 3636 Dihedral : 4.098 23.677 3172 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.15), residues: 3032 helix: 2.36 (0.11), residues: 2368 sheet: -0.62 (0.65), residues: 84 loop : -1.55 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 518 TYR 0.025 0.002 TYR B 535 PHE 0.022 0.002 PHE B 631 TRP 0.031 0.002 TRP D 773 HIS 0.007 0.001 HIS C 612 Details of bonding type rmsd covalent geometry : bond 0.00434 (20024) covalent geometry : angle 0.59138 (27632) hydrogen bonds : bond 0.03305 ( 1656) hydrogen bonds : angle 4.14705 ( 4944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3792.07 seconds wall clock time: 65 minutes 48.77 seconds (3948.77 seconds total)