Starting phenix.real_space_refine on Tue May 20 12:04:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sl8_40575/05_2025/8sl8_40575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sl8_40575/05_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_40575/05_2025/8sl8_40575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sl8_40575/05_2025/8sl8_40575.map" model { file = "/net/cci-nas-00/data/ceres_data/8sl8_40575/05_2025/8sl8_40575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sl8_40575/05_2025/8sl8_40575.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19688 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: {'GLN:plan1': 22, 'HIS:plan': 12, 'TYR:plan': 11, 'ASN:plan1': 8, 'TRP:plan': 7, 'ASP:plan': 23, 'PHE:plan': 27, 'GLU:plan': 40, 'ARG:plan': 35} Unresolved non-hydrogen planarities: 878 Restraints were copied for chains: C, B, D Time building chain proxies: 11.20, per 1000 atoms: 0.57 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: 5.34 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 2.52 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: 7.06 Time building geometry restraints manager: 6.14 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 2.610 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: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 45.230 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.001 TRP B 636 HIS 0.005 0.001 HIS A 998 PHE 0.014 0.001 PHE C 994 TYR 0.010 0.001 TYR D 535 ARG 0.002 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.13659 ( 1656) hydrogen bonds : angle 5.87416 ( 4944) covalent geometry : bond 0.00365 (20024) covalent geometry : angle 0.67758 (27632) *********************** 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 : 2.394 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: 0.2368 time to fit residues: 77.5060 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 : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 10.0000 chunk 236 optimal weight: 40.0000 chunk 131 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 50.0000 chunk 126 optimal weight: 50.0000 chunk 244 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 283 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 HIS B 528 ASN B 602 ASN A 439 HIS A 528 ASN A 602 ASN C 439 HIS C 528 ASN C 602 ASN C1048 GLN D 439 HIS D 528 ASN D 602 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.072107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.053936 restraints weight = 158234.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.055098 restraints weight = 96524.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.055828 restraints weight = 69754.018| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20024 Z= 0.123 Angle : 0.472 6.437 27632 Z= 0.262 Chirality : 0.036 0.163 3484 Planarity : 0.003 0.037 3636 Dihedral : 3.951 23.156 3172 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.34 % Allowed : 4.83 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.15), residues: 3032 helix: 1.87 (0.10), residues: 2360 sheet: 0.32 (0.58), residues: 84 loop : -1.34 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 605 HIS 0.005 0.001 HIS C 998 PHE 0.011 0.001 PHE B 631 TYR 0.012 0.001 TYR A 535 ARG 0.004 0.000 ARG B 518 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 1656) hydrogen bonds : angle 3.89888 ( 4944) covalent geometry : bond 0.00250 (20024) covalent geometry : angle 0.47199 (27632) *********************** 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 198 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 194 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 422 TYR cc_start: 0.8341 (m-80) cc_final: 0.7267 (m-80) REVERT: B 773 TRP cc_start: 0.8286 (m100) cc_final: 0.7654 (m100) REVERT: B 842 MET cc_start: 0.9049 (mmp) cc_final: 0.8818 (mmp) REVERT: B 1057 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8376 (tp40) REVERT: A 842 MET cc_start: 0.8949 (mmp) cc_final: 0.8720 (mmp) REVERT: A 1057 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8374 (tp40) REVERT: C 422 TYR cc_start: 0.8350 (m-80) cc_final: 0.7276 (m-80) REVERT: C 773 TRP cc_start: 0.8310 (m100) cc_final: 0.7471 (m100) REVERT: C 1057 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8407 (tp40) REVERT: D 422 TYR cc_start: 0.8458 (m-80) cc_final: 0.7399 (m-80) REVERT: D 634 LYS cc_start: 0.9256 (tmtt) cc_final: 0.9042 (tptp) REVERT: D 773 TRP cc_start: 0.8236 (m100) cc_final: 0.7412 (m100) REVERT: D 1057 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8448 (tp40) outliers start: 4 outliers final: 0 residues processed: 198 average time/residue: 0.2420 time to fit residues: 81.6220 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 : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 284 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 287 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 ASN A 612 HIS C 528 ASN C 612 HIS D 528 ASN D 612 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.071411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.053280 restraints weight = 158146.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.054462 restraints weight = 95440.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.055210 restraints weight = 68607.831| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20024 Z= 0.150 Angle : 0.487 6.617 27632 Z= 0.269 Chirality : 0.036 0.170 3484 Planarity : 0.003 0.036 3636 Dihedral : 3.853 23.775 3172 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.25 % Allowed : 4.75 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.15), residues: 3032 helix: 2.43 (0.11), residues: 2344 sheet: 0.62 (0.62), residues: 84 loop : -1.35 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 517 HIS 0.004 0.001 HIS C 998 PHE 0.015 0.001 PHE A 631 TYR 0.018 0.002 TYR D 535 ARG 0.003 0.000 ARG C 518 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 1656) hydrogen bonds : angle 3.75533 ( 4944) covalent geometry : bond 0.00295 (20024) covalent geometry : angle 0.48729 (27632) *********************** 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 175 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 2.075 Fit side-chains REVERT: B 773 TRP cc_start: 0.8403 (m100) cc_final: 0.7727 (m100) REVERT: B 1057 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8410 (tp40) REVERT: A 1057 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8432 (tp40) REVERT: C 842 MET cc_start: 0.8761 (mmp) cc_final: 0.8498 (mmp) REVERT: C 1057 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8449 (tp40) REVERT: D 422 TYR cc_start: 0.8558 (m-80) cc_final: 0.8339 (m-80) REVERT: D 634 LYS cc_start: 0.9267 (tmtt) cc_final: 0.9046 (tptp) REVERT: D 842 MET cc_start: 0.8924 (mmp) cc_final: 0.8672 (mmp) REVERT: D 1057 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8482 (tp40) outliers start: 3 outliers final: 2 residues processed: 175 average time/residue: 0.2150 time to fit residues: 65.8117 Evaluate side-chains 142 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 189 optimal weight: 2.9990 chunk 72 optimal weight: 50.0000 chunk 145 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 205 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 269 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 612 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.070938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.052829 restraints weight = 159444.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.054344 restraints weight = 103331.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.054667 restraints weight = 66963.484| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20024 Z= 0.165 Angle : 0.507 7.725 27632 Z= 0.275 Chirality : 0.037 0.166 3484 Planarity : 0.004 0.037 3636 Dihedral : 3.938 22.328 3172 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.15), residues: 3032 helix: 2.43 (0.10), residues: 2360 sheet: 0.52 (0.65), residues: 84 loop : -1.24 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 517 HIS 0.004 0.001 HIS C 998 PHE 0.017 0.002 PHE C 631 TYR 0.018 0.001 TYR A 535 ARG 0.003 0.000 ARG C 518 Details of bonding type rmsd hydrogen bonds : bond 0.02948 ( 1656) hydrogen bonds : angle 3.79104 ( 4944) covalent geometry : bond 0.00324 (20024) covalent geometry : angle 0.50674 (27632) *********************** 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 166 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 2.149 Fit side-chains REVERT: B 422 TYR cc_start: 0.8577 (m-80) cc_final: 0.7424 (m-80) REVERT: B 842 MET cc_start: 0.8904 (mmp) cc_final: 0.8655 (mmp) REVERT: B 1057 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8439 (tp40) REVERT: A 842 MET cc_start: 0.8850 (mmp) cc_final: 0.8608 (mmp) REVERT: A 1057 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8486 (tp40) REVERT: C 634 LYS cc_start: 0.9290 (tmtt) cc_final: 0.9087 (tptp) REVERT: C 1057 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8472 (tp40) REVERT: D 422 TYR cc_start: 0.8606 (m-80) cc_final: 0.8374 (m-80) REVERT: D 634 LYS cc_start: 0.9251 (tmtt) cc_final: 0.9037 (tptp) REVERT: D 1057 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8397 (tp40) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2265 time to fit residues: 65.9105 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 : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 122 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 187 optimal weight: 0.0970 chunk 259 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 94 optimal weight: 0.2980 chunk 236 optimal weight: 50.0000 chunk 246 optimal weight: 30.0000 chunk 71 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.072555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.054301 restraints weight = 158185.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.055513 restraints weight = 95094.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.056265 restraints weight = 68478.999| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20024 Z= 0.098 Angle : 0.445 6.384 27632 Z= 0.238 Chirality : 0.035 0.127 3484 Planarity : 0.003 0.036 3636 Dihedral : 3.639 20.317 3172 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.16), residues: 3032 helix: 2.71 (0.11), residues: 2364 sheet: 0.77 (0.65), residues: 84 loop : -1.30 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1053 HIS 0.002 0.000 HIS C 998 PHE 0.008 0.001 PHE D 583 TYR 0.009 0.001 TYR D 535 ARG 0.002 0.000 ARG C 518 Details of bonding type rmsd hydrogen bonds : bond 0.02568 ( 1656) hydrogen bonds : angle 3.42406 ( 4944) covalent geometry : bond 0.00199 (20024) covalent geometry : angle 0.44535 (27632) *********************** 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 175 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 2.406 Fit side-chains revert: symmetry clash REVERT: B 398 PHE cc_start: 0.8107 (m-80) cc_final: 0.7647 (m-80) REVERT: B 422 TYR cc_start: 0.8520 (m-80) cc_final: 0.7413 (m-80) REVERT: B 842 MET cc_start: 0.8920 (mmp) cc_final: 0.8703 (mmp) REVERT: A 422 TYR cc_start: 0.8457 (m-80) cc_final: 0.7177 (m-80) REVERT: C 422 TYR cc_start: 0.8456 (m-80) cc_final: 0.7370 (m-80) REVERT: D 422 TYR cc_start: 0.8514 (m-80) cc_final: 0.8231 (m-80) REVERT: D 634 LYS cc_start: 0.9259 (tmtt) cc_final: 0.9032 (tptp) REVERT: D 842 MET cc_start: 0.8924 (mmp) cc_final: 0.8604 (mmp) REVERT: D 1057 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8480 (tp40) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2355 time to fit residues: 72.0199 Evaluate side-chains 144 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 206 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 226 optimal weight: 8.9990 chunk 258 optimal weight: 3.9990 chunk 155 optimal weight: 30.0000 chunk 237 optimal weight: 50.0000 chunk 272 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.068657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.050475 restraints weight = 162286.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.051630 restraints weight = 97786.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.052357 restraints weight = 70695.221| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20024 Z= 0.307 Angle : 0.668 7.961 27632 Z= 0.372 Chirality : 0.040 0.139 3484 Planarity : 0.005 0.059 3636 Dihedral : 4.585 25.396 3172 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.15), residues: 3032 helix: 1.95 (0.11), residues: 2344 sheet: 0.10 (0.66), residues: 84 loop : -1.38 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 773 HIS 0.011 0.002 HIS C 612 PHE 0.031 0.003 PHE B 631 TYR 0.029 0.003 TYR A 535 ARG 0.007 0.001 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 1656) hydrogen bonds : angle 4.52882 ( 4944) covalent geometry : bond 0.00579 (20024) covalent geometry : angle 0.66845 (27632) *********************** 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 159 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 2.259 Fit side-chains REVERT: B 398 PHE cc_start: 0.8217 (m-80) cc_final: 0.8012 (m-80) REVERT: A 398 PHE cc_start: 0.8484 (m-80) cc_final: 0.8254 (m-80) REVERT: C 398 PHE cc_start: 0.8382 (m-80) cc_final: 0.8115 (m-80) REVERT: D 634 LYS cc_start: 0.9358 (tmtt) cc_final: 0.9136 (tptp) REVERT: D 1057 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8316 (mm-40) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2239 time to fit residues: 63.6046 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 : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 92 optimal weight: 8.9990 chunk 81 optimal weight: 50.0000 chunk 4 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 309 optimal weight: 0.9990 chunk 155 optimal weight: 30.0000 chunk 230 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.070673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.052329 restraints weight = 158470.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.053531 restraints weight = 95597.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.054285 restraints weight = 68799.938| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20024 Z= 0.161 Angle : 0.519 6.951 27632 Z= 0.278 Chirality : 0.036 0.137 3484 Planarity : 0.003 0.036 3636 Dihedral : 4.083 23.300 3172 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.15), residues: 3032 helix: 2.40 (0.11), residues: 2352 sheet: -0.02 (0.66), residues: 84 loop : -1.34 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 523 HIS 0.005 0.001 HIS C 612 PHE 0.013 0.001 PHE A 631 TYR 0.017 0.001 TYR D 535 ARG 0.003 0.000 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.03009 ( 1656) hydrogen bonds : angle 3.86573 ( 4944) covalent geometry : bond 0.00318 (20024) covalent geometry : angle 0.51872 (27632) *********************** 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 165 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 2.212 Fit side-chains REVERT: B 1057 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8360 (tp40) REVERT: A 398 PHE cc_start: 0.8401 (m-80) cc_final: 0.8141 (m-80) REVERT: D 422 TYR cc_start: 0.8577 (m-80) cc_final: 0.8204 (m-80) REVERT: D 634 LYS cc_start: 0.9307 (tmtt) cc_final: 0.9101 (tptp) REVERT: D 1057 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8375 (tp40) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.2196 time to fit residues: 64.8989 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 : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 131 optimal weight: 20.0000 chunk 293 optimal weight: 20.0000 chunk 286 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 0.0020 chunk 38 optimal weight: 9.9990 chunk 250 optimal weight: 50.0000 chunk 248 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 overall best weight: 5.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 423 HIS ** B1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 HIS ** A1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3715 r_free = 0.3715 target = 0.068886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.050668 restraints weight = 162493.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.051850 restraints weight = 97583.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.052590 restraints weight = 70057.626| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20024 Z= 0.276 Angle : 0.640 8.579 27632 Z= 0.354 Chirality : 0.039 0.128 3484 Planarity : 0.004 0.041 3636 Dihedral : 4.513 25.483 3172 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.15), residues: 3032 helix: 2.00 (0.11), residues: 2344 sheet: -0.50 (0.65), residues: 84 loop : -1.65 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 361 HIS 0.010 0.002 HIS C 612 PHE 0.025 0.002 PHE B 631 TYR 0.026 0.002 TYR D 535 ARG 0.004 0.001 ARG A 518 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 1656) hydrogen bonds : angle 4.47864 ( 4944) covalent geometry : bond 0.00527 (20024) covalent geometry : angle 0.64007 (27632) *********************** 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 161 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 2.492 Fit side-chains REVERT: B 398 PHE cc_start: 0.8227 (m-80) cc_final: 0.7809 (m-10) REVERT: B 1057 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8335 (tp40) REVERT: A 398 PHE cc_start: 0.8404 (m-80) cc_final: 0.8174 (m-80) REVERT: D 398 PHE cc_start: 0.8425 (m-80) cc_final: 0.8209 (m-80) REVERT: D 634 LYS cc_start: 0.9341 (tmtt) cc_final: 0.9129 (tptp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2247 time to fit residues: 64.9537 Evaluate side-chains 131 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 107 optimal weight: 10.0000 chunk 32 optimal weight: 0.3980 chunk 250 optimal weight: 0.5980 chunk 260 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 153 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 137 optimal weight: 0.0980 chunk 236 optimal weight: 10.0000 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.071885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.053544 restraints weight = 156212.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.054741 restraints weight = 94401.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.055494 restraints weight = 68254.196| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4062 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= 0.102 Angle : 0.495 7.622 27632 Z= 0.258 Chirality : 0.035 0.126 3484 Planarity : 0.003 0.036 3636 Dihedral : 3.877 22.179 3172 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.15), residues: 3032 helix: 2.57 (0.11), residues: 2364 sheet: -0.34 (0.65), residues: 84 loop : -1.51 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D1053 HIS 0.003 0.001 HIS C 998 PHE 0.010 0.001 PHE D 841 TYR 0.012 0.001 TYR A 587 ARG 0.005 0.000 ARG C 518 Details of bonding type rmsd hydrogen bonds : bond 0.02772 ( 1656) hydrogen bonds : angle 3.62949 ( 4944) covalent geometry : bond 0.00206 (20024) covalent geometry : angle 0.49506 (27632) *********************** 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 171 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 2.123 Fit side-chains REVERT: B 398 PHE cc_start: 0.8402 (m-80) cc_final: 0.7967 (m-80) REVERT: B 422 TYR cc_start: 0.8696 (m-80) cc_final: 0.7520 (m-80) REVERT: B 1057 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8517 (tp40) REVERT: C 422 TYR cc_start: 0.8648 (m-80) cc_final: 0.7439 (m-80) REVERT: D 634 LYS cc_start: 0.9311 (tmtt) cc_final: 0.9086 (tptp) REVERT: D 1057 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8743 (tp40) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2155 time to fit residues: 65.0093 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 : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 55 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 303 optimal weight: 40.0000 chunk 106 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 288 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 241 optimal weight: 0.5980 chunk 245 optimal weight: 9.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.070279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.052007 restraints weight = 160313.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.053207 restraints weight = 96010.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.053962 restraints weight = 68936.837| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20024 Z= 0.182 Angle : 0.547 8.152 27632 Z= 0.293 Chirality : 0.037 0.136 3484 Planarity : 0.003 0.036 3636 Dihedral : 3.978 23.152 3172 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.16), residues: 3032 helix: 2.51 (0.11), residues: 2356 sheet: -0.58 (0.64), residues: 84 loop : -1.51 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 361 HIS 0.007 0.001 HIS C 612 PHE 0.018 0.002 PHE A 631 TYR 0.020 0.002 TYR D 535 ARG 0.003 0.000 ARG D 518 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 1656) hydrogen bonds : angle 3.92079 ( 4944) covalent geometry : bond 0.00356 (20024) covalent geometry : angle 0.54664 (27632) ********************** 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 162 residues out of total 2752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 2.302 Fit side-chains REVERT: B 398 PHE cc_start: 0.8239 (m-80) cc_final: 0.7827 (m-80) REVERT: B 1057 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8346 (tp40) REVERT: A 398 PHE cc_start: 0.8364 (m-80) cc_final: 0.7885 (m-80) REVERT: D 398 PHE cc_start: 0.8481 (m-80) cc_final: 0.8270 (m-80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2191 time to fit residues: 63.7857 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 : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 187 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 35 optimal weight: 0.0980 chunk 38 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 144 optimal weight: 50.0000 chunk 230 optimal weight: 3.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.070619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.052486 restraints weight = 160399.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.053929 restraints weight = 102726.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.054374 restraints weight = 67368.170| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20024 Z= 0.157 Angle : 0.528 7.570 27632 Z= 0.280 Chirality : 0.036 0.127 3484 Planarity : 0.003 0.037 3636 Dihedral : 3.927 22.494 3172 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.15), residues: 3032 helix: 2.54 (0.11), residues: 2360 sheet: -0.63 (0.63), residues: 84 loop : -1.51 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 361 HIS 0.006 0.001 HIS C 612 PHE 0.015 0.001 PHE B 631 TYR 0.017 0.002 TYR C 535 ARG 0.003 0.000 ARG C 518 Details of bonding type rmsd hydrogen bonds : bond 0.02919 ( 1656) hydrogen bonds : angle 3.83255 ( 4944) covalent geometry : bond 0.00311 (20024) covalent geometry : angle 0.52764 (27632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6072.18 seconds wall clock time: 106 minutes 15.78 seconds (6375.78 seconds total)